CAZypedia - User contributions [en-ca]

Polysaccharide Lyase Family 1

2015-08-06T14:23:36Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' ''Anti''-β-elimination reaction catalysed by pectate lyase. R and R’ represent additional galacturonan residues]]
The PL1 family polysaccharide lyases ([http://www.cazy.org/PL1.html PL1]) harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-{{smallcaps|d}}-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end ([http://www.enzyme-database.org/query.php?ec=4.2.2.2 EC 4.2.2.2]) <cite>Albersheim1962, Edstrom1964a, Edstrom1964b</cite>. Pectin lyases differ from pectate lyases as they are active against a substrate bearing methyl-ester groups at C6 ([http://www.enzyme-database.org/query.php?ec=4.2.2.10 EC 4.2.2.10]). The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman <cite>Gerlt1993</cite>.

== Catalytic Residues ==
[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using ''Bacillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modeled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. Abstraction of the C5 proton is by the catalytic arginine, the Brønstead base <cite>Scavetta1999, Herron2000, Seyedarabi2010</cite>. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) <cite>Yoder1993</cite> and PelE (exo-acting) <cite>Lietzke1994</cite> from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite> ([{{PDBlink}} 2pec], [{{PDBlink}} 2pcu], [{{PDBlink}} 1bn8]). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed <cite>Mayans1997, Vitali1998</cite>, they are closely similar to pectate lyase have the arginine acting as Brønstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim <cite>Albersheim1962</cite>.
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine <cite>Scavetta1999, Herron2000</cite>, the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Brønstead base <cite>Charnock2002</cite>. More detailed information on specificity emerged from a more recent study <cite>Seyedarabi2010</cite> which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function <cite>Pickersgill1994</cite>. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction <cite>Scavetta1999, Herron2000</cite>.
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC <cite>Yoder1993</cite> and PelE <cite>Lietzke1994</cite>, and ''Bacillus subtilis'' pectate lyase <cite>Pickersgill1994</cite>.

== References ==
<biblio>
#Albersheim1962 pmid=13860094
#Edstrom1964a pmid=14235515
#Edstrom1964b pmid=14235514
#Gerlt1993 pmid=8218268
#Scavetta1999 pmid=10368179
#Herron2000 pmid=10922032
#Seyedarabi2010 pmid=20000851
#Yoder1993 pmid=8502994
#Lietzke1994 pmid=12232373
#Pickersgill1994 pmid=7634076
#Mayans1997 pmid=9195887
#Vitali1998 pmid=9449837
#Charnock2002 pmid=12221284
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-31T10:31:48Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' Reaction catalysed by pectate lyase ]]

In the figure (Fig. 1) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic arginine, the Bronstead base [6-8]. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

[[Image:PL1_active_site_crop.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using B''acillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modelled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC [9]and PelE [10], and ''Bacillus subtilis'' pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

File:PL1 active site crop.jpg

2015-07-31T10:31:23Z

Richard Pickersgill:

Polysaccharide Lyase Family 1

2015-07-31T09:09:28Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px|'''Figure 1.''' Reaction catalysed by pectate lyase ]]

In the figure (Fig. 1) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic arginine, the Bronstead base [6-8]. The ''Bacillus subtilis'' Michaelis complex is shown in Fig. 2. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

[[Image:PL1_active_site.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using B''acillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modelled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC [9]and PelE [10], and ''Bacillus subtilis'' pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-31T09:06:45Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px| ]]

In the figure (right) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

[[Image:PL1_active_site.jpg|thumb|400px|'''Figure 2.''' Michaelis complex formed using B''acillus subtilis'' pectate lyase R279A mutant and trigalacturonic acid. The galacturonan residues are labelled according to the subsites they bind: -1, +1, +2. The catalytic arginine is modelled back in the position seen in the native structure and is close to the C5 proton abstracted. The two "catalytic" calcium-ions bound between enzyme and substrate carboxylates that acidify the C5 proton are Ca2 and Ca3.]]

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC [9]and PelE [10], and ''Bacillus subtilis'' pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-31T09:01:36Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px| ]]

In the figure (right) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

[[Image:PL1_active_site.jpg|thumb|400px|'''Figure X.''' Figure legend. ]]

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC [9]and PelE [10], and ''Bacillus subtilis'' pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-31T08:58:30Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px| ]]

In the figure (right) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

[[Image:PL1_active_site.jpg|thumb|400px| ]]

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC [9]and PelE [10], and ''Bacillus subtilis'' pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

File:PL1 active site.jpg

2015-07-31T08:56:49Z

Richard Pickersgill:

Polysaccharide Lyase Family 1

2015-07-29T14:46:17Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness ''anti''-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px| ]]

In the figure (right) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates ''anti''-β-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC [9]and PelE [10], and ''Bacillus subtilis'' pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-29T14:42:15Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness anti-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px| ]]

In the figure (right) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates anti-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic Arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from ''Erwinia chrysanthemi'', and endo-acting ''Bacillus subtilis'' pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;First catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC [9]and PelE [10], and ''Bacillus subtilis'' pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-29T14:41:17Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness anti-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px| ]]

In the figure (right) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates anti-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic Arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from Erwinia chrysanthemi, and endo-acting Bacillus subtilis pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;FFirst catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: ''Erwinia chrysanthemi'' pectate lyases: PelC [9]and PelE [10], and Bacillus subtilis pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-29T14:40:20Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness anti-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px| ]]

In the figure (right) showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates anti-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic Arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from Erwinia chrysanthemi, and endo-acting Bacillus subtilis pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;FFirst catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: Erwinia chrysanthemi pectate lyases: PelC [9]and PelE [10], and Bacillus subtilis pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-29T14:39:42Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness anti-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px| ]]

In the figure right showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates anti-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic Arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from Erwinia chrysanthemi, and endo-acting Bacillus subtilis pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;FFirst catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: Erwinia chrysanthemi pectate lyases: PelC [9]and PelE [10], and Bacillus subtilis pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-29T14:39:05Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness anti-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|400px| ]]

In the figure above showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates anti-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic Arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from Erwinia chrysanthemi, and endo-acting Bacillus subtilis pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;FFirst catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: Erwinia chrysanthemi pectate lyases: PelC [9]and PelE [10], and Bacillus subtilis pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-29T14:38:33Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness anti-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:Reaction.jpg|thumb|200px| ]]

In the figure above showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates anti-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic Arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from Erwinia chrysanthemi, and endo-acting Bacillus subtilis pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;FFirst catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: Erwinia chrysanthemi pectate lyases: PelC [9]and PelE [10], and Bacillus subtilis pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-29T14:32:56Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness anti-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

[[Image:reaction.jpeg|thumb|200px| ]]

In the figure above showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates anti-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic Arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from Erwinia chrysanthemi, and endo-acting Bacillus subtilis pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;FFirst catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: Erwinia chrysanthemi pectate lyases: PelC [9]and PelE [10], and Bacillus subtilis pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

File:Reaction.jpg

2015-07-29T14:24:21Z

Richard Pickersgill:

File:Clip image002.png

2015-07-29T14:20:17Z

Richard Pickersgill:

Polysaccharide Lyase Family 1

2015-07-29T14:16:08Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness anti-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

!--[if !mso]> ![endif]-->[[File:C:\Users\Richard\AppData\Local\Temp\msohtmlclip1\01\clip_image002.png|442px]]

In the figure above showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates anti-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic Arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from Erwinia chrysanthemi, and endo-acting Bacillus subtilis pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;FFirst catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: Erwinia chrysanthemi pectate lyases: PelC [9]and PelE [10], and Bacillus subtilis pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-29T14:07:20Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness anti-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

In the figure above showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates anti-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic Arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from Erwinia chrysanthemi, and endo-acting Bacillus subtilis pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;First catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;FFirst catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: Erwinia chrysanthemi pectate lyases: PelC [9]and PelE [10], and Bacillus subtilis pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Polysaccharide Lyase Family 1

2015-07-29T14:06:45Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]:
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL1'''
|-
|'''3-D Structure'''
|β-helix
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|calcium
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL1.html
|}
</div>


== Substrate specificities ==
The PL1 family polysaccharide lyases harness anti-β-elimination chemistry to cleave 1,4-linked α-D-galacturonan to produce oligosaccharides with an unsaturated hexenuronic acid residue and a new reducing end [1-3].

In the figure above showing pectate lyase activity R and R’ are additional galacturonan residues. Pectin lyases are active against a substrate bearing methyl-ester groups at C6. The geometry of the α1,4-linkage facilitates anti-elimination about the C4-glycosidic oxygen bond.

== Kinetics and Mechanism ==
The mechanism involves acidification of the C5 proton of the galacturonan residue binding to the +1 subsite of the enzyme, abstraction of this acidified proton, and subsequent leaving group elimination. The leaving group provides a new reducing end and the group from which it was eliminated has an unsaturated C4-C5 bond. The mechanism of proton abstraction from carbon acids is discussed by Gerlt and Gassman [4, 5].

== Catalytic Residues ==
Acidification of the C5 proton in the polysaccharide family 1 enzymes is by the binding of two “catalytic” calcium-ions which are bound only in the Michaelis complex and not to the free enzyme [6-8]. Abstraction of the C5 proton is by the catalytic Arginine, the Bronstead base [6-8]. Protonation of the leaving group is probably by solvent water, though other possibilities have been discussed in the literature.

== Three-dimensional structures ==
Pectate lyases PelC (endo-acting) [9] and PelE (exo-acting) [10] from Erwinia chrysanthemi, and endo-acting Bacillus subtilis pectate lyase [11] (PDB codes: 2PEC, 1PCL, 1BN8). These structures were remarkable in showing the polypeptide chain folded into a right-handed superhelix comprising three β-strands per turn with turns stacking to form a domain of three parallel β-sheets. The structures showed that parallel β-sheets are stable in the absence of protecting α-helices and revealed remarkable side-chain stacks particularly in the hydrophobic interior. Structures of pectin lyase followed [12, 13], they are closely similar to pectate lyase have the arginine acting as Bronstead base but also have more hydrophobic active centres suitable for binding methylated pectin.

== Family Firsts ==
;First description of catalytic activity: Pectin trans-eliminase activity was first demonstrated in 1962 by Albersheim [1].
;FFirst catalytic base identification: Arginine emerged as the catalytic base from the complex of PelC with pentagalacturonate formed using the inactive mutant in which the arginine was substituted by lysine [6, 7], the structure showed that the arginine would be in the correct position to abstract the C5 proton. Comparison of PL10 and PL1 Michaelis complexes cemented the role of the arginine as Bronstead base [14]. More detailed information on specificity emerged from a more recent study [8] which showed the central three subsites bound galacturonsyl-residues, but that the more remote subsites could tolerate methylated galacturonsyl-residues.
;FFirst catalytic divalent cation identification: The importance of acidifying the C5 proton by stabilizing the charge on the substrate carboxylate was acknowledged early though the conserved arginine was originally thought to fulfil this function [11]. It was later shown that two catalytic calcium-ions bound in the Michaelis complex acidify the C5 proton facilitating its abstraction [6, 7].
;First 3-D structures: Erwinia chrysanthemi pectate lyases: PelC [9]and PelE [10], and Bacillus subtilis pectate lyase [11].

== References ==
<biblio>
1. Albersheim, P. and U. Killias, Studies relating to the purification and properties of pectin transeliminase. Archives of biochemistry and biophysics, 1962. 97: p. 107-15.

2. Edstrom, R.D. and H.J. Phaff, ELIMINATIVE CLEAVAGE OF PECTIN AND OF OLIGOGALACTURONIDE METHYL ESTERS BY PECTIN TRANS-ELIMINASE. The Journal of biological chemistry, 1964. 239: p. 2409-15.

3. Edstrom, R.D. and H.J. Phaff, PURIFICATION AND CERTAIN PROPERTIES OF PECTIN TRANS-ELIMINASE FROM ASPERGILLUS FONSECAEUS. The Journal of biological chemistry, 1964. 239: p. 2403-8.

4. Gerlt, J.A. and P.G. Gassman, UNDERSTANDING ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - DETAILS OF STEPWISE MECHANISMS FOR BETA-ELIMINATION REACTIONS. Journal of the American Chemical Society, 1992. 114(15): p. 5928-5934.

5. Gerlt, J.A. and P.G. Gassman, AN EXPLANATION FOR RAPID ENZYME-CATALYZED PROTON ABSTRACTION FROM CARBON ACIDS - IMPORTANCE OF LATE TRANSITION-STATES IN CONCERTED MECHANISMS. Journal of the American Chemical Society, 1993. 115(24): p. 11552-11568.

6. Scavetta, R.D., et al., Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 1999. 11(6): p. 1081-1092.

7. Herron, S.R., et al., Structure and function of pectic enzymes: Virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America, 2000. 97(16): p. 8762-8769.

8. Seyedarabi, A., et al., Structural Insights into Substrate Specificity and the anti beta-Elimination Mechanism of Pectate Lyase. Biochemistry, 2010. 49(3): p. 539-546.

9. Yoder, M.D., N.T. Keen, and F. Jurnak, NEW DOMAIN MOTIF - THE STRUCTURE OF PECTATE LYASE-C, A SECRETED PLANT VIRULENCE FACTOR. Science, 1993. 260(5113): p. 1503-1507.

10. Lietzke, S.E., et al., THE 3-DIMENSIONAL STRUCTURE OF PECTATE LYASE-E, A PLANT VIRULENCE FACTOR FROM ERWINIA-CHRYSANTHEMI. Plant Physiology, 1994. 106(3): p. 849-862.

11. Pickersgill, R., et al., THE STRUCTURE OF BACILLUS-SUBTILIS PECTATE LYASE IN COMPLEX WITH CALCIUM. Nature Structural Biology, 1994. 1(10): p. 717-723.

12. Mayans, O., et al., Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure, 1997. 5(5): p. 677-689.

13. Vitali, J., et al., The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-angstrom resolution. Plant Physiology, 1998. 116(1): p. 69-80.

14. Charnock, S.J., et al., Convergent evolution sheds light on the anti-beta-elimination mechanism common to family 1 and 10 polysaccharide lyases. Proceedings of the National Academy of Sciences of the United States of America, 2002. 99(19): p. 12067-12072.
</biblio>

[[Category:Polysaccharide Lyase Families|PL001]]

Glycoside Hydrolase Family 28

2010-02-16T18:19:49Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the general acid (proton donor), while Asp180 (Asp202) and Asp202 (Asp224) active the catalytic water molecule (numbers are given for Aspergillus niger and in parantheses for Ewinia carotovora polygalacturonase).

== Three-dimensional structures ==
The structure of rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite> revealed the signature parallel beta-helix architecture common to several pectin active enzymes including family 1 pectate lyases. The GH28 enzymes are distinguished from the lyases by having four, not three, parallel beta-sheets extending along their longitudinal axes. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of beta-helix having ten tuns, not eleven <cite>5</cite>. The structure of exopolygalacturonase from Yersinia enterocolitica shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=9135118
#8 pmid=17397864
#9 pmid=12022868

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-16T18:15:24Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the general acid (proton donor), while Asp180 (Asp202) and Asp202 (Asp224) active the catalytic water molecule (numbers are given for Aspergillus niger and in parantheses for Ewinia carotovora polygalacturonase).

== Three-dimensional structures ==
The structure of rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite> revealed the signature parallel beta-helix architecture common to several pectin active enzymes including family 1 pectate lyases. The GH28 enzymes are distinguished from the lyases by having four, not three, parallel beta-sheets extending along their longitudinal axes. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of beta-helix having ten tuns, not eleven <cite>5</cite>. The structure of exopolygalacturonase from Yersinia enterocolitica shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=9135118
#8 pmid=17397864
#9 pmid=12022868
#10 pmid=14623112

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-16T18:13:33Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the general acid (proton donor), while Asp180 (Asp202) and Asp202 (Asp224) active the catalytic water molecule (numbers are given for Aspergillus niger and in parantheses for Ewinia carotovora polygalacturonase).

== Three-dimensional structures ==
The structure of rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite> revealed the signature parallel beta-helix architecture common to several pectin active enzymes including family 1 pectate lyases. The GH28 enzymes are distinguished from the lyases by having four, not three, parallel beta-sheets extending along their longitudinal axes. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of beta-helix having ten tuns, not eleven <cite>5</cite>. The structure of exopolygalacturonase from Yersinia enterocolitica shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>10</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=9135118
#8 pmid=17397864
#9 pmid=12022868
#10 pmid=14623112

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-16T18:10:59Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the general acid (proton donor), while Asp180 (Asp202) and Asp202 (Asp224) active the catalytic water molecule (numbers are given for Aspergillus niger and in parantheses for Ewinia carotovora polygalacturonase).

== Three-dimensional structures ==
The structure of rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite> revealed the signature parallel beta-helix architecture common to several pectin active enzymes including family 1 pectate lyases. The GH28 enzymes are distinguished from the lyases by four, not three, parallel beta-sheets extending along their longitudinal axes. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of beta-helix having ten tuns, not eleven <cite>5</cite>. The structure of exopolygalacturonase from Yersinia enterocolitica shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>10</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=9135118
#8 pmid=17397864
#9 pmid=12022868
#10 pmid=14623112

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-16T17:59:26Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the general acid (proton donor), while Asp180 (Asp202) and Asp202 (Asp224) active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
The structure of rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite> revealed the signature parallel beta-helix architecture common to several pectin active enzymes including family 1 pectate lyases. The GH28 enzymes are distinguished from the lyases by their four, not three, parallel beta-sheets extending along the longitudinal axis. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of beta-helix having ten tuns, not eleven <cite>5</cite>. The structure fo exopolygalacturonase from Yersinia enterocolitica shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>8</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>9</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>10</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=9135118
#8 pmid=17397864
#9 pmid=12022868
#10 pmid=14623112

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-16T17:58:27Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the general acid (proton donor), while Asp180 (Asp202) and Asp202 (Asp224) active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
The structure of rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite> revealed the signature parallel beta-helix architecture common to several pectin active enzymes including family 1 pectate lyases. The GH28 enzymes are distinguished from the lyases by their four, not three, parallel beta-sheets extending along the longitudinal axis. Compared to rhamnogalacturonase, polygalacturonase lacks the C-terminal turn of beta-helix having ten tuns, not eleven <cite>5</cite>. The structure fo exopolygalacturonase from Yersinia enterocolitica shows how amino acid inserts close off the open substrate binding cleft of endopolygalacturonase to form an exopolygalacturonase <cite>10</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=9135118
#8 pmid=12022868
#9 pmid=14623112
#10 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-16T17:52:22Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the general acid (proton donor), while Asp180 (Asp202) and Asp202 (Asp224) active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
The structure of rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite> revealed the signature parallel beta-helix architecture of several pectin active enzymes including family 1 pectate lyases. The GH28 enzymes are distinguished from the lyases in they have four parallel beta-sheets extending longitudinally along the length. per endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus niger <cite>6</cite>, endopolygalacturonase from Stereum purpureum <cite>8</cite>, endopolygalacturonase I (a processive enzyme) from Aspergillus niger <cite>9</cite>, exopolygalacturonase from Yersinia enterocolitica <cite>10</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=9135118
#8 pmid=12022868
#9 pmid=14623112
#10 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-16T17:46:37Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. These authors identified Asp202, Asp223 and Asp224 as the catalytic residues. The clearest assignment of the role of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 (Asp223) is proposed to act as the general acid (proton donor), while Asp180 (Asp202) and Asp202 (Asp224) active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus niger <cite>6</cite>, endopolygalacturonase from Stereum purpureum <cite>8</cite>, endopolygalacturonase I (a processive enzyme) from Aspergillus niger <cite>9</cite>, exopolygalacturonase from Yersinia enterocolitica <cite>10</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=9135118
#8 pmid=12022868
#9 pmid=14623112
#10 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-16T17:44:42Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus niger <cite>6</cite>, endopolygalacturonase from Stereum purpureum <cite>8</cite>, endopolygalacturonase I (a processive enzyme) from Aspergillus niger <cite>9</cite>, exopolygalacturonase from Yersinia enterocolitica <cite>10</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (223) is proposed to act as the catalytic acid (proton donor), while Asp180 (202) and Asp202 (224) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=9135118
#8 pmid=12022868
#9 pmid=14623112
#10 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-16T16:39:36Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite> based on the results of mutagenesis and comparison with phage 22 tailspike protein <cite>7</cite>. Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus niger <cite>6</cite>, endopolygalacturonase from Stereum purpureum <cite>8</cite>, endopolygalacturonase I (a processive enzyme) from Aspergillus niger <cite>9</cite>, exopolygalacturonase from Yersinia enterocolitica <cite>10</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=9135118
#8 pmid=12022868
#9 pmid=14623112
#10 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-15T17:57:47Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus niger <cite>6</cite>, endopolygalacturonase from Stereum purpureum <cite>7</cite>, endopolygalacturonase I (a processive enzyme) from Aspergillus niger <cite>8</cite>, exopolygalacturonase from Yersinia enterocolitica <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=12022868
#8 pmid=14623112
#9 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-15T17:55:49Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are [[inverting enzymes]]; they harness a [[single displacement mechanism]] as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus niger <cite>6</cite>, endopolygalacturonase from Stereum purpureum <cite>7</cite>, endopolygalacturonase I (a processive enzyme) from Aspergillus niger <cite>8</cite>, exopolygalacturonase from Yersinia enterocolitica <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=12022868
#8 pmid=14623112
#9 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

User:Richard Pickersgill

2010-02-15T13:49:15Z

Richard Pickersgill:

I have a continuing interest in the structure and function of CAZy enzymes. I can be contacted at Queen Mary University of London. E: r.w.pickersgill@qmul.ac.uk; T: +44 (0)20 7882 8444.

User:Richard Pickersgill

2010-02-15T13:48:13Z

Richard Pickersgill: Created page with 'Richard Pickersgill I have a continuing interest in the structure and function of CAZy enzymes. I can be contacted at Queen Mary University of London. E: r.w.pickersgill@qmul.a…'

Richard Pickersgill

I have a continuing interest in the structure and function of CAZy enzymes. I can be contacted at Queen Mary University of London. E: r.w.pickersgill@qmul.ac.uk; T: +44 (0)20 7882 8444.

Glycoside Hydrolase Family 28

2010-02-15T13:41:27Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus niger <cite>6</cite>, endopolygalacturonase from Stereum purpureum <cite>7</cite>, endopolygalacturonase I (a processive enzyme) from Aspergillus niger <cite>8</cite>, exopolygalacturonase from Yersinia enterocolitica <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: Aspergillus niger endopolygalacturonase. Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and in parentheses for Erwinia carotovora polygalacturonase) <cite>6</cite>.
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure, Erwinia carotovora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=12022868
#8 pmid=14623112
#9 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-15T13:34:28Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus niger <cite>6</cite>, endopolygalacturonase from Stereum purpureum <cite>7</cite>, endopolygalacturonase I (a processive enzyme) from Aspergillus niger <cite>8</cite>, exopolygalacturonase from Yersinia enterocolitica <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora polygalacturonase residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=12022868
#8 pmid=14623112
#9 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-15T13:33:32Z

Richard Pickersgill:

Normal 0



{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus niger <cite>6</cite>, endopolygalacturonase from Stereum purpureum <cite>7</cite>, endopolygalacturonase I (a processive enzyme) from Aspergillus niger <cite>8</cite>, exopolygalacturonase from Yersinia enterocolitica <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora polygalacturonase residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam. ISBN 0-444-82330-1
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=12022868
#8 pmid=14623112
#9 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-15T13:26:27Z

Richard Pickersgill:

Normal 0



{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus niger <cite>6</cite>, endopolygalacturonase from Stereum purpureum <cite>7</cite>, endopolygalacturonase I (a processive enzyme) from Aspergillus niger <cite>8</cite>, exopolygalacturonase from Yersinia enterocolitica <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora polygalacturonase residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Normal 0 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam.
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=12022868
#8 pmid=14623112
#9 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-15T12:42:36Z

Richard Pickersgill:

Normal 0



{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus ? <cite>6</cite>, endopolygalacturonase from ? <cite>7</cite>, endopolygalacturonase I from Aspergillus ? <cite>8</cite>, exopolygalacturonase from ? <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora polygalacturonase residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1 Normal 0 Visser, J. and Voragen, V.D.J., Eds. (1996) Pectin and Pectinases, Elsevier, Amsterdam.
#2 pmid=8605979
#3 pmid=9464254
#4 pmid=9115442
#5 pmid=9733763
#6 pmid=10521427
#7 pmid=12022868
#8 pmid=
#9 pmid=17397864

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-14T20:20:45Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endopolygalacturonase from Erwinia carotovora <cite>5</cite>, endopolygalacturonase II from Aspergillus ? <cite>6</cite>, endopolygalacturonase from ? <cite>7</cite>, endopolygalacturonase I from Aspergillus ? <cite>8</cite>, exopolygalacturonase from ? <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora polygalacturonase residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1
#2
#3
#4
#5
#6
#7
#8
#9

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-14T20:18:20Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endo-polygalacturonase from Erwinia carotovora <cite>5</cite>, endo-polygalacturonase II from Aspergillus ? <cite>6</cite>, endogalacturonase from ? <cite>7</cite>, endo-polygalacturonase I from Aspergillus ? <cite>8</cite>, exogalacturonase from ? <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora polygalacturonase residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1
#2
#3
#4
#5
#6
#7
#8
#9

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-14T20:15:41Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. It was subsequently realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases <cite>5</cite>. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endo-polygalacturonase from Erwinia carotovora <cite>5</cite>, endo-polygalacturonase II from Aspergillus ? <cite>6</cite>, endogalacturonase from ? <cite>7</cite>, endo-polygalacturonase I from Aspergillus ? <cite>8</cite>, exogalacturonase from ? <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1
#2
#3
#4
#5
#6
#7
#8
#9

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-14T20:13:32Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. Pickersgill et al <cite>5</cite> realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endo-polygalacturonase from Erwinia carotovora <cite>5</cite>, endo-polygalacturonase II from Aspergillus ? <cite>6</cite>, endogalacturonase from ? <cite>7</cite>, endo-polygalacturonase I from Aspergillus ? <cite>8</cite>, exogalacturonase from ? <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>8</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>9</cite>.

== References ==
<biblio>
#1
#2
#3
#4
#5
#6
#7
#8
#9

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-14T20:10:02Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. Pickersgill et al <cite>5</cite> realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endo-polygalacturonase from Erwinia carotovora <cite>5</cite>, endo-polygalacturonase II from Aspergillus ? <cite>6</cite>, endogalacturonase from ? <cite>7</cite>, endo-polygalacturonase I from Aspergillus ? <cite>8</cite>, exogalacturonase from ? <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>7</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.

== References ==
<biblio>
#1
#2
#3
#4
#5
#6
#7
#8
#9

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-14T20:07:52Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. Pickersgill et al <cite>5</cite> realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endo-polygalacturonase from Erwinia carotovora <cite>5</cite>, endo-polygalacturonase II from Aspergillus ? <cite>6</cite>, endogalacturonase from ? <cite>7</cite>, endo-polygalacturonase I from Aspergillus ? <cite>8</cite>, exogalacturonase from ? <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>7</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.

== References ==
<biblio>
#Comfort2007 pmid=17323919
#He1999 pmid=9312086
#3 isbn=978-0-240-52118-3
#MikesClassic Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-14T20:06:03Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>3</cite>. References that are not in PubMed can be typed in by hand <cite>MikesClassic</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. Pickersgill et al <cite>5</cite> realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endo-polygalacturonase from Erwinia carotovora <cite>5</cite>, endo-polygalacturonase II from Aspergillus ? <cite>6</cite>, endogalacturonase from ? <cite>7</cite>, endo-polygalacturonase I from Aspergillus ? <cite>8</cite>, exogalacturonase from ? <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <cite>6</cite>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>7</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.

== References ==
<biblio>
#Comfort2007 pmid=17323919
#He1999 pmid=9312086
#3 isbn=978-0-240-52118-3
#MikesClassic Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-14T20:02:50Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan <cite>1</cite>.

This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>3</cite>. References that are not in PubMed can be typed in by hand <cite>MikesClassic</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures <cite>2</cite>. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide <cite>3</cite>.

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis <cite>4</cite>. Pickersgill et al <cite>5</cite> realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases. The clearest assignment of the catalytic residues comes from the work of van Santen et al <cite>6</cite>; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==
Rhamnogalacturonase (RGase A) from Aspergillus aculeatus <cite>4</cite>, endo-polygalacturonase from Erwinia carotovora <cite>5</cite>, endo-polygalacturonase II from Aspergillus ? <cite>6</cite>, endogalacturonase from ? <cite>7</cite>, endo-polygalacturonase I from Aspergillus ? <cite>8</cite>, exogalacturonase from ? <cite>9</cite>.

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis <cite>2</cite>.
;First [[catalytic acid]] identification: van Santen et al <site>6</site>; Asp201 (197) is proposed to act as the catalytic acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora residues in parentheses).
;First 3-D structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus <cite>4</cite>. First polygalacturonase structure: Erwinia carotavora polygalacturonase <cite>5</cite>.
;First complexes: Product complex (+1 subsite) and a complex including a furanose isomer (-1) <cite>7</cite>. A product complex in an exo-polygalacturonase illuminates the structural basis for its exo-activity <cite>8</cite>.

== References ==
<biblio>
#Comfort2007 pmid=17323919
#He1999 pmid=9312086
#3 isbn=978-0-240-52118-3
#MikesClassic Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-14T19:41:45Z

Richard Pickersgill:

{{UnderConstruction}}
* [[Author]]: ^^^Richard Pickersgill^^^
* [[Responsible Curator]]: ^^^Richard Pickersgill^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH28'''
|-
|'''Clan'''
|GH-N
|-
|'''Mechanism'''
|inverting
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |http://www.cazy.org/fam/GH28.html
|}
</div>


== Substrate specificities ==
The overwhelming majority of enzymes in this family are polygalacturonases. They hydrolyse the alpha-1,4 glycosidic linkage between galacturonate residues in polygalacturonic acid. Both endo and exo acting polygalacturonases are represented. Polygalacturonic acid, with varying degrees of C6 methylation and acetylation, forms the smooth homogalacturonan region of pectin. There are also some enzymes in this family active against rhamnogalacturonan which forms the branched part of the pectin molecule. Rhamnogalacturonases cleave the alpha-1,2 linkage between galacturonic acid and rhamnose residues. Two other enzymes rhamnohydrolase and rhamnogalacturonan galacturonohydrolase cleave off single terminal carbohydrate units, rhamnose and galacturonate respectively, from the non-reducing end of rhamnogalacturonan [1].

This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>3</cite>. References that are not in PubMed can be typed in by hand <cite>MikesClassic</cite>.

== Kinetics and Mechanism ==
Family GH28 enzymes are inverting enzymes; they harness a single displacement mechanism as revealed by 1H-NMR spectroscopy of the products of hydrolysis in D2O reaction mixtures [2]. Subsequently, the rhamnogalacturonases were also shown to invert the configuration of the newly formed reducing end of the polysaccharide [3].

== Catalytic Residues ==
The crystal structure of rhamnogalacturonase revealed the cluster of aspartates involved in catalysis [4]. Pickersgill et al [5] realised that protonation of the glycosidic oxygen and nucleophilic attack at the anomeric carbon may be from the same side of the bond in alpha-linked polysaccharides rather than opposite sides with a resulting shorter separation of carboxylates than standard for cleaving substrates with beta-linkages explaining the short spacing between the conserved carboxylates in the GH28 hydrolases [5]. The clearest assignment of the catalytic residues comes from the work of van Santen et al [6]; Asp201 is proposed to act as the general acid (proton donor), while Asp180 and Asp202 active the catalytic water molecule (numbers are given for Aspergillus niger polygalacturonase).

== Three-dimensional structures ==

== Family Firsts ==
;First sterochemistry determination: Endopolygalacturonases from Aspergillus niger and Aspergillus tubingensis [2]<cite>Comfort2007</cite>.
;First [[catalytic nucleophile]] identification: van Santen et al [6]; Asp201 (197) is proposed to act as the acid (proton donor), while Asp180 (180) and Asp202 (198) active the catalytic water molecule (numbers are given for the Aspergillus niger and Erwinia carotavora residues in parentheses). <cite>MikesClassic</cite>.
;First [[general acid/base]] residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.
;First 3-D structure: First GH28 family structure: Rhamnogalacturonase (RGase-A) from Aspergillus aculeatus [4]. First polygalacturonase structure: Erwinia carotavora polygalacturonase [5]<cite>3</cite>.

== References ==
<biblio>
#Comfort2007 pmid=17323919
#He1999 pmid=9312086
#3 isbn=978-0-240-52118-3
#MikesClassic Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]

</biblio>

[[Category:Glycoside Hydrolase Families|GH028]]

Glycoside Hydrolase Family 28

2010-02-14T19:30:48Z

Richard Pickersgill: