CAZypedia - User contributions [en-ca]

Glycoside Hydrolase Family 35

2011-03-21T09:22:25Z

Anna Kulminskaya:

{{CuratorApproved}}
* [[Author]]s: ^^^Anna Kulminskaya^^^, ^^^Mirko Maksimainen^^^, ^^^Juha Rouvinen^^^
* [[Responsible Curator]]: ^^^Anna Kulminskaya^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH35'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH35.html
|}
</div>


== Substrate specificities ==
The majority of GH35 members are β-galactosidases (EC [{{EClink}}3.2.1.23 3.2.1.23]). GH35 enzymes have been isolated from microorganisms such as fungi, bacteria and yeasts, as well as higher organisms such as plants, animals, and human cells. These β-galactosidases catalyse the hydrolysis of terminal non-reducing β-D-galactose residues in, for example, lactose (1,4-O-β-D-galactopyranosyl-D-glucose), oligosaccharides, glycolipids, and glycoproteins. Various GH35 β-galactosidases demonstrate specificity towards β1,3-, β1,6- or β1,4-galactosidic linkages <cite>Zinin2002, Gamauf2007, Tanthanuch2008</cite>, and are often most active under acidic conditions <cite>Zhang1994, vanCasteren2000, Wang2009</cite>. As with many other CAZy families <cite>GeislerLee2006, Henrissat2001, Tuskan2006</cite>, GH35 members tend to be represented by multi-gene families in plants <cite>Ahn2007, Smith2000, Lazan2004, Ross1994, Tanthanuch2008</cite>. Moreover, plant GH35 β-galactosidases have be divided into two classes: members of the first are capable of hydrolyzing pectic β-1,4-galactans, while those of the second can specifically cleave β-1,3- and β1,6-galactosyl linkages of arabinogalactan proteins <cite>Kotake2005</cite>.

In addition to β-galactosidases, GH35 also contains a limited number of archeal exo-β-glucosaminidases (EC [{{EClink}}3.2.1.165 3.2.1.165]) <cite>Tanaka2003 Liu2006</cite>. Such enzymes hydrolyze chitosan or chitosan oligosaccharides to remove successive D-glucosamine residues from non-reducing termini.

== Kinetics and Mechanism ==
Beta-galactosidases of GH35 catalyze the hydrolysis of terminal β-galactosyl residues via a double-displacement mechanism, which leads to net retention of the β-anomeric configuration of the released galactose molecule. The stereochemistry of the reaction was first shown by NMR for the human β-galactosidase precursor <cite>Zhang1994</cite> and has been subsequently confirmed by other investigators for microbial and plant enzymes <cite>vanCasteren2000, Zinin2002</cite> .

== Catalytic Residues ==
The catalytic residues for family 35 were first predicted on the basis of hydrophobic cluster analysis of proteins of similar protein fold <cite>Henrissat1995</cite>. Experimentally, the glutamic acid residue 268 was first identified as the catalytic nucleophile in human lysosomal β-galactosidase precursor using a slow substrate, 2,4-dinitrophenyl-2-deoxy-2-fluoro-β-D-galactopyranoside, that allowed trapping of a covalent glycosyl-enzyme intermediate and subsequent peptide mapping <cite>McCarter1997</cite>. This approach was repeated for two bacterial β-galactosidases from ''Xanthomonas manihotis'' and ''Bacillus circulans'' <cite>Blanchard2001</cite>. The general acid/base catalyst was inferred to be Glu200 from structural studies of a ''Penicillium'' sp. β-galactosidase <cite>Rojas2004</cite>. Recent structural studies (''vide infra'') revealed two different conformations of the general acid/base catalyst in the β-galactosidase of ''Trichoderma reesei'' <cite> Maksimainen2010</cite>.

== Three-dimensional structures ==
The first 3D-structures of a GH35 enzyme, those of a β-galactosidase from ''Pencillium'' sp. (Psp-β-gal) in native (PDB [{{PDBlink}}1tg7 1tg7]) and product-complexed (PDB [{{PDBlink}}1xc6 1xc6]) forms, were reported in 2004 at 1.90 Å and 2.10 Å resolution, respectively <cite>Rojas2004</cite>. The structure of a β-galactosidase from ''Bacteriodes thetaiotamicron'' (Btm-β-gal) was subsequently reported by the New York Structural GenomiX Research Consortium in 2008 at 2.15 Å resolution (PDB [{{PDBlink}}3d3a 3d3a]). In 2010, an atomic (1.2 Å) resolution crystal structure of a ''Trichoderma reesei'' (''Hypocrea jecorina'') β-galactosidase (Tr-β-gal, PDB [{{PDBlink}}3og2 3og2]) was reported, together with complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4 Å resolutions, respectively (PDB codes [{{PDBlink}}3ogr 3ogr], [{{PDBlink}}3ogs 3ogs], and [{{PDBlink}}3ogv 3ogv], respectively) <cite>Maksimainen2010</cite>.

GH35 enzymes belong to Clan GH-A, and thus have an (α/β)<sub>8</sub> (TIM) barrel as the catalytic domain, in which two glutamic acid residues act as the general acid-base and nucleophilic catalysts. These residues are located in strands 4 and 7 of the barrel.

The comparison of the native structures of Psp-β-gal, Tr-β-gal and Btmβ-gal reveals two things ('''Figure 1'''): Firstly, Btm-β-gal consists of three distinct domains, whereas Psp-β-gal and Tr-β-gal consist of five and six domains, respectively. The second and third domains of Btm-β-gal are quite similar with the fourth and fifth domains of Psp-β-gal, and with the fifth and sixth domains of Tr-β-gal. Secondly, major structural differences between Psp-β-gal and Tr-β-gal are in the conformations of the loop regions. Although the crystal structures of Psp-β-gal and Tr-β-gal are similar, the interpretation of the structure of Tr-β-gal is somewhat different from that presented earlier for Psp-β-gal: Rojas et al. considered Psp-β-gal to be composed of five distinct structural domains. The overall structure is built around the first, TIM barrel, domain. Domain 2 is an all β-sheet domain containing an immunoglobulin-like subdomain, Domain 3 is based on a Greek-key β-sandwich, and Domains 4 and 5 are jelly rolls <cite>Rojas2004</cite>. In contrast, Maksimainen et al. concluded the domain 2 includes two different domains and thus the Tr-β-gal and Psp-β-gal structures both form six similar domains <cite>Maksimainen2010</cite>.

The superimposition of the active sites of the GH35 β-galactosidases shows a remarkable similarity. In addition to the catalytic residues, the active sites of the GH35 β-galactosidases contain many identical residues ('''Figure 1B'''). Based on the galactose-bound crystallographic models of Psp-β-gal and Tr-β-gal, a single galactose molecule is bound to the active site of the GH35 enzyme in the chair conformation in the β-anomeric configuration.

Additionally, Maksimainen et al. have described conformational changes in two loop regions of the active site of Tr-β-gal, that implicates a conformational selection mechanism for the enzyme (Figure 2). Unlike the induced fit theory, which assumes that the initial interaction between a protein and its binding partner induces a conformational change in the protein through a stepwise process, the conformational selection theory is based on the assumption that the unbound protein exists as an ensemble of conformations in dynamic equilibrium. Interaction between a weakly populated, higher-energy conformation and a binding partner causes the equilibrium to move in favor of the selected conformation <cite>Tsai1999, Boehr2008</cite>. This can be seen in the structures of Tr-β-gal: the open and closed conformation are both favorable in the native structure and the closed conformation becomes more favorable in the complex structures. Furthermore, The acid/base catalyst Glu200 has two different conformations in the IPTG and PETG complex structures that clearly affects the p''K''<sub>a</sub> value of this residue and thus the catalytic mechanism of the enzyme <cite>Maksimainen2010</cite>.

=== Structure images ===

[[Image: GH35 comparison.png|thumb|left|750px|'''Figure 1. Comparison of the native structures of GH35 β-galactosidases.''' A. Global structures, B. Active sites. Psp-β-gal (PDB code [{{PDBlink}}1tg7 1tg7]), Tr-β-gal (PDB code [{{PDBlink}}3og2 3og2]) and Btm-β-gal (PDB code [{{PDBlink}}3d3a 3d3a]) are colored in green, brown and blue, respectively.]]

[[Image: Conformational selection.png|thumb|left|750px| '''Figure 2. Illustration of the conformational selection mechanism observed in Tr-β-gal <cite>Maksimainen2010</cite>.''']]

<br style="clear: both" />

== Family Firsts ==
;First stereochemistry determination:
Human β-galactosidase precursor by NMR <cite>Zhang1994</cite>

;First catalytic nucleophile identification:
Human β-galactosidase precursor by 2-fluorogalactose labeling <cite>McCarter1997</cite>.

;First general acid/base residue identification:
''Penicillium sp.'' β-galactosidase by structural identification <cite>Rojas2004</cite>.

;First 3-D structure:
''Penicillium sp.'' β-galactosidase <cite>Rojas2004</cite>.

== References ==
<biblio>
#Ahn2007 pmid=17466346
#Smith2000 pmid=10889266
#Lazan2004 pmid=15694277
#Ross1994 pmid=7991682
#Tanthanuch2008 pmid=18664295
#Tanka2003 pmid=12923090
#Liu2006 pmid=16912928
#Zhang1994 pmid=7998946
#Henrissat1995 pmid=7624375
#McCarter1997 pmid=8995274
#Rojas2004 pmid=15491613
#Blanchard2001 pmid=11423106
#Maksimainen2010 Maksimainen M, Hakulinen N, Kallio JM, Timoharju T, Turunen O, Rouvinen J. ''Crystal structures of Trichoderma reesei beta-galactosidase reveal conformational changes in the active site.'' J Struct Biol. Apr; 174(1): 156-63. //''Note: Due to a problem with PubMed data, this reference is not automatically formatted. Please see these links out:'' [http://dx.doi.org/10.1016/j.jsb.2010.11.024 DOI:10.1016/j.jsb.2010.11.024] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21130883 PMID:21130883]
#GeislerLee2006 pmid=16415215
#Henrissat2001 pmid=11554480
#Tuskan2006 pmid=16973872
#Gamauf2007 pmid=17381511
#Zinin2002 pmid=11909597
#vanCasteren2000 pmid=11086688
#Wang2009 pmid=19453169
#Kotake2005 pmid=15980190
#Boehr2008 Boehr DD, Wright PE ''How do proteins interact?'' Science 2008, 320 1429-1430.
#Tsai1999 pmid=10468538
</biblio>

[[Category:Glycoside Hydrolase Families|GH035]]

User:Anna Kulminskaya

2011-03-02T13:07:35Z

Anna Kulminskaya:

I’m a research scientist at the Petersburg Nuclear Physics Institute, Molecular and Radiation Biophysics Department, Russia. I received my PhD degree [[Image:AKulminskaya.jpg|thumb|ширинаpx| ]]under supervision of Neustroev Kirill studying the exo-inulinase from ''Aspergillus awamori'' ([[GH32]]). Now I’m a leader of the Laboratory of Enzymology at the same Institute.

The main research area of our team is carbohydrate enzymology and applications. We focus in understanding the way in which particular enzymes act to alter the structure of poly- or oligosaccharides found in Nature, and to harness these enzymes for practical applications. Using the tools of chemo-organic synthesis and biochemistry, our work aims to provide increased understanding of the chemical principles underlying mechanisms of action of glycoside hydrolases with transglycosylating activity.

We are particularly interested in the alpha-galactosidases ([[GH27]] and [[GH36]]), beta-galactosidase ([[GH35]]), beta-xylosidases ([[GH3]]), beta-xylanases, cellulose-degrading enzymes, alpha- or beta-mannosidases ([[GH2]]) and alpha-L-fucosidases.

[[Category:Contributors|Kulminskaya,Anna]]

User:Anna Kulminskaya

2011-03-02T12:56:39Z

Anna Kulminskaya:

[[File:I]]’m a research scientist at the Petersburg Nuclear Physics Institute, Molecular and Radiation Biophysics Department, Russia. I received my PhD degree under supervision of Neustroev Kirill studying the exo-inulinase from ''Aspergillus awamori'' ([[GH32]]). Now I’m a leader of the Laboratory of Enzymology at the same Institute.

The main research area of our team is carbohydrate enzymology and applications. We focus in understanding the way in which particular enzymes act to alter the structure of poly- or oligosaccharides found in Nature, and to harness these enzymes for practical applications. Using the tools of chemo-organic synthesis and biochemistry, our work aims to provide increased understanding of the chemical principles underlying mechanisms of action of glycoside hydrolases with transglycosylating activity.

We are particularly interested in the alpha-galactosidases ([[GH27]] and [[GH36]]), beta-galactosidase ([[GH35]]), beta-xylosidases ([[GH3]]), beta-xylanases, cellulose-degrading enzymes, alpha- or beta-mannosidases ([[GH2]]) and alpha-L-fucosidases.

[[Category:Contributors|Kulminskaya,Anna]]

File:AKulminskaya.jpg

2011-03-02T12:54:28Z

Anna Kulminskaya:

Glycoside Hydrolase Family 35

2011-02-14T14:06:21Z

Anna Kulminskaya:

{{UnderConstruction}}
* [[Author]]: ^^^Anna Kulminskaya^^^
* [[Responsible Curator]]: ^^^Anna Kulminskaya^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH35'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH35.html
|}
</div>


== Substrate specificities ==
The majority of GH35 members are β-galactosidases (EC [{{EClink}}3.2.1.23 3.2.1.23]). GH35 enzymes have been isolated from microorganisms such as fungi, bacteria and yeasts, as well as higher organisms such as plants, animals, and human cells. These β-galactosidases catalyse the hydrolysis of terminal non-reducing β-D-galactose residues in, for example, lactose (1,4-O-β-D-galactopyranosyl-D-glucose), oligosaccharides, glycolipids, and glycoproteins. Various GH35 β-galactosidases demonstrate specificity towards β1,3-, β1,6- or β1,4-galactosidic linkages <cite>Zinin2002, Gamauf2007, Tanthanuch2008</cite>, and are often most active under acidic conditions <cite>Zhang1994, vanCasteren2000, Wang2009</cite>. As with many other CAZy families <cite>GeislerLee2006, Henrissat2001, Tuskan2006</cite>, GH35 members tend to be represented by multi-gene families in plants <cite>Ahn2007, Smith2000, Lazan2004, Ross1994, Tanthanuch2008</cite>. Moreover, plant GH35 β-galactosidases have be divided into two classes: members of the first are capable of hydrolyzing pectic β-1,4-galactans, while those of the second can specifically cleave β-1,3- and β1,6-galactosyl linkages of arabinogalactan proteins <cite>Kotake2005</cite>.

In addition to β-galactosidases, GH35 also contains a limited number of archeal exo-β-glucosaminidases (EC [{{EClink}}3.2.1.165 3.2.1.165]) <cite>Tanaka2003 Liu2006</cite>. Such enzymes hydrolyze chitosan or chitosan oligosaccharides to remove successive D-glucosamine residues from non-reducing termini.

== Kinetics and Mechanism ==
Beta-galactosidases of GH35 catalyze the hydrolysis of terminal β-galactosyl residues via a double-displacement mechanism, which leads to net retention of the β-anomeric configuration of the released galactose molecule. The stereochemistry of the reaction was first shown by NMR for the human β-galactosidase precursor <cite>Zhang1994</cite> and has been subsequently confirmed by other investigators for microbial and plant enzymes <cite>vanCasteren2000, Zinin2002</cite> .

== Catalytic Residues ==
The catalytic residues for family 35 were first predicted on the basis of hydrophobic cluster analysis of proteins of similar protein fold <cite>Henrissat1995</cite>. Experimentally, the glutamic acid residue 268 was first identified as the catalytic nucleophile in human lysosomal β-galactosidase precursor using a slow substrate, 2,4-dinitrophenyl-2-deoxy-2-fluoro- β-D-galactopyranoside, that allowed trapping of a covalent glycosyl-enzyme intermediate. This allowed subsequent peptide mapping to exactly identify the catalytic nucleophile <cite>McCarter1997</cite>. Subsequently, this approach was repeated for two bacterial β-galactosidases from ''Xanthomonas manihotis'' and ''Bacillus circulans'' <cite>Blanchard2001</cite>. The general acid/base catalyst was inferred to be Glu200 from structural studies of a ''Penicillium'' sp. β-galactosidase <cite>Rojas2004</cite>. Recent structural studies <cite>Maksimainen2010</cite> revealed two different conformations of the general acid/base catalyst in the β-galactosidase of ''Trichoderma reesei''.

== Three-dimensional structures ==
As of February 2011, only three enzymes from GH35 have been structurally characterized. The first 3D-structures of a GH35 enzyme, those of a β-galactosidase from ''Pencillium'' sp. (Psp-β-gal) in native (PDB [{{PDBlink}}1tg7 1tg7]) and product-complexed (PDB [{{PDBlink}}1xc6 1xc6]) forms, were reported in 2004 at 1.90 Å and 2.10 Å resolution, respectively <cite>Rojas2004</cite>. The structure of a β-galactosidase from ''Bacteriodes thetaiotamicron'' was subsequently reported by the New York Structural GenomiX Research Consortium in 2008 at 2.15 Å resolution (PDB [{{PDBlink}}3d3a 3d3a]). In 2010, a high (1.2 Å) resolution crystal structure of a ''Trichoderma reesei'' (''Hypocrea jecorina'') β-galactosidase (Tr-β-gal, PDB [{{PDBlink}}3og2 3og2]) was reported, together with complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4 Å resolutions, respectively (PDB codes [{{PDBlink}}3ogr 3ogr], [{{PDBlink}}3ogs 3ogs], and [{{PDBlink}}3ogv 3ogv], respectively) <cite>Maksimainen2010</cite>.

GH35 enzymes belong to Clan GH-A, and thus have a (α/β)<sub>8</sub> TIM barrel comprising the catalytic domain. A structural analysis of the galactose-binding active-site was based on the comparison of the crystallographic models of the native Psp-β-gal and Tr-β-gal enzymes and their respective complexes with galactose. A single galactose molecule is bound to the TIM barrel domain of the enzyme in the chair conformation in the β-anomeric configuration. Two glutamic acid residues act as the general acid-base and nucleophilic catalysts; these are presented on strands 4 and 7 of the barrel.Although the crystal structures of Psp-β-gal and Tr-β-gal are similar, interpretation of the structure of Tr-β-gal is somewhat different from that presented earlier for Psp-β-gal: Rojas et al. considered Psp-β-gal to be composed of five distinct structural domains. The overall structure is built around the first, TIM barrel, domain. Domain 2 us an all β-sheet domain containing an immunoglobulin-like subdomain, domain 3 is based on a Greek-key β-sandwich and domains 4 and 5 are jelly rolls <cite>Rojas2004</cite>. In contrast, Maksimainen et al. concluded that the Tr-β-gal and Psp-β-gal structures both form six similar domains and <cite>Maksimainen2010</cite>. The most of the structural differences between them are in the conformations of the loop regions.

Additionally, Maksimainen et al. have described conformational changes in two loop regions of the active site of Tr-β-gal, thus implicating a conformational selection mechanism for the enzyme. The acid/base catalyst Glu200 exhibited two different conformations which affect the p''K''<sub>a</sub> value of this residue and thus the catalytic mechanism.

== Family Firsts ==
;First stereochemistry determination:
Human β-galactosidase precursor by NMR <cite>Zhang1994</cite>

;First catalytic nucleophile identification:
Human β-galactosidase precursor by 2-fluorogalactose labeling <cite>McCarter1997</cite>.

;First general acid/base residue identification:
''Penicillium sp.'' β-galactosidase by structural identification <cite>Rojas2004</cite>.

;First 3-D structure:
''Penicillium sp.'' β-galactosidase <cite>Rojas2004</cite>.

== References ==
<biblio>
#Ahn2007 pmid=17466346
#Smith2000 pmid=10889266
#Lazan2004 pmid=15694277
#Ross1994 pmid=7991682
#Tanthanuch2008 pmid=18664295
#Tanka2003 pmid=12923090
#Liu2006 pmid=16912928
#Zhang1994 pmid=7998946
#Henrissat1995 pmid=7624375
#McCarter1997 pmid=8995274
#Rojas2004 pmid=15491613
#Blanchard2001 pmid=11423106
#Maksimainen2010 Maksimainen M, Hakulinen N, Kallio JM, Timoharju T, Turunen O, Rouvinen J. ''Crystal structures of Trichoderma reesei beta-galactosidase reveal conformational changes in the active site.'' J Struct Biol. 2010, ''in press.'' //''Note: Due to a problem with PubMed data, this reference is not automatically formatted. Please see these links out:'' [http://dx.doi.org/10.1016/j.jsb.2010.11.024 DOI:10.1016/j.jsb.2010.11.024] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21130883 PMID:21130883]
#GeislerLee2006 pmid=16415215
#Henrissat2001 pmid=11554480
#Tuskan2006 pmid=16973872
#Gamauf2007 pmid=17381511
#Zinin2002 pmid=11909597
#vanCasteren2000 pmid=11086688
#Wang2009 pmid=19453169
#Kotake2005 pmid=15980190
</biblio>

[[Category:Glycoside Hydrolase Families|GH035]]

Glycoside Hydrolase Family 35

2011-02-08T13:50:11Z

Anna Kulminskaya:

{{UnderConstruction}}
* [[Author]]: ^^^Anna Kulminskaya^^^
* [[Responsible Curator]]: ^^^Anna Kulminskaya^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH35'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH35.html
|}
</div>


== Substrate specificities ==
The majority of GH35 members are β-galactosidases (EC [{{EClink}}3.2.1.23 3.2.1.23]). GH35 enzymes have been isolated from microorganisms such as fungi, bacteria and yeasts, as well as higher organisms such as plants, animals, and human cells. These β-galactosidases catalyse the hydrolysis of terminal non-reducing β-D-galactose residues in, for example, lactose (1,4-O-β-D-galactopyranosyl-D-glucose), oligosaccharides, glycolipids, and glycoproteins. Various GH35 β-galactosidases demonstrate specificity towards β1,3-, β1,6- or β1,4-galactosidic linkages <cite>Zinin2002, Gamauf2007, Tanthanuch2008</cite>, and are often most active under acidic conditions <cite>Zhang1994, van Casteren2000, Wang2009</cite>. As with many other CAZy families <cite>GeislerLee2006, Henrissat2001, Tuskan2006</cite>, GH35 members tend to be represented by multi-gene families in plants <cite>Ahn2007, Smith2000, Lazan2004, Ross1994, Tanthanuch2008</cite>. Moreover, plant GH35 β-galactosidases have be divided into two classes: members of the first are capable of hydrolyzing pectic β-1,4-galactans, while those of the second can specifically cleave β-1,3- and β1,6-galactosyl linkages of arabinogalactan proteins <cite>Kotake2005</cite>.

In addition to β-galactosidases, GH35 also contains a limited number of archeal exo-β-glucosaminidases (EC [{{EClink}}3.2.1.165 3.2.1.165]) <cite>Tanaka2003 Liu2006</cite>. Such enzymes hydrolyze chitosan or chitosan oligosaccharides to remove successive D-glucosamine residues from non-reducing termini.

== Kinetics and Mechanism ==
Beta-galactosidases of GH35 catalyze the hydrolysis of terminal β-galactosyl residues via a double-displacement mechanism, which leads to net retention of the β-anomeric configuration of the released galactose molecule. The stereochemistry of the reaction was first shown by NMR for the human β-galactosidase precursor <cite>Zhang1994</cite> and has been subsequently confirmed by other investigators for microbial and plant enzymes <cite>Casteren2000, Zinin2002</cite> .

== Catalytic Residues ==
The catalytic residues for family 35 were first predicted on the basis of hydrophobic cluster analysis of proteins of similar protein fold <cite>Henrissat1995</cite>. Experimentally, the glutamic acid residue 268 was first identified as the catalytic nucleophile in human lysosomal β-galactosidase precursor using a slow substrate, 2,4-dinitrophenyl-2-deoxy-2-fluoro- β-D-galactopyranoside, that allowed trapping of a covalent glycosyl-enzyme intermediate. This allowed subsequent peptide mapping to exactly identify the catalytic nucleophile <cite>McCarter1997</cite>. Subsequently, this approach was repeated for two bacterial β-galactosidases from ''Xanthomonas manihotis'' and ''Bacillus circulans'' <cite>Blanchard2001</cite>. The general acid/base catalyst was inferred to be Glu200 from structural studies of a ''Penicillium'' sp. β-galactosidase <cite>Rojas2004</cite>. Recent structural studies <cite>Maksimainen2010</cite> revealed two different conformations of the general acid/base catalyst in the β-galactosidase of ''Trichoderma reesei''.

== Three-dimensional structures ==
As of February 2011, only three enzymes from GH35 have been structurally characterized. The first 3D-structures of a GH35 enzyme, those of a β-galactosidase from ''Pencillium'' sp. (Psp-β-gal) in native (PDB [{{PDBlink}}1tg7 1tg7]) and product-complexed (PDB [{{PDBlink}}1xc6 1xc6]) forms, were reported in 2004 at 1.90 Å and 2.10 Å resolution, respectively <cite>Rojas2004</cite>. The structure of a β-galactosidase from ''Bacteriodes thetaiotamicron'' was subsequently reported by the New York Structural GenomiX Research Consortium in 2008 at 2.15 Å resolution (PDB [{{PDBlink}}3d3a 3d3a]). In 2010, a high (1.2 Å) resolution crystal structure of a ''Trichoderma reesei'' (''Hypocrea jecorina'') β-galactosidase (Tr-β-gal, PDB [{{PDBlink}}3og2 3og2]) was reported, together with complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4 Å resolutions, respectively (PDB codes [{{PDBlink}}3ogr 3ogr], [{{PDBlink}}3ogs 3ogs], and [{{PDBlink}}3ogv 3ogv], respectively) <cite>Maksimainen2010</cite>.

GH35 enzymes belong to Clan GH-A, and thus have a (α/β)<sub>8</sub> TIM barrel comprising the catalytic domain. A structural analysis of the galactose-binding active-site was based on the comparison of the crystallographic models of the native Psp-β-gal and Tr-β-gal enzymes and their respective complexes with galactose. A single galactose molecule is bound to the TIM barrel domain of the enzyme in the chair conformation in the β-anomeric configuration. Two glutamic acid residues act as the general acid-base and nucleophilic catalysts; these are presented on strands 4 and 7 of the barrel. Although the crystal structures of Psp-β-gal and Tr-β-gal are similar, interpretation of the structure of Tr-β-gal is somewhat different from that presented earlier for Psp-β-gal: Rojas et al. considered Psp-β-gal to be divided into five domains combining the second and the third domain, although they form separate sub-units in the structure <cite>Rojas2004</cite>. In contrast, Maksimainen et al. concluded that the Tr-β-gal structure contains a central catalytic α/β-barrel surrounded by a horseshoe consisting of five anti-parallel β-sandwich structures <cite>Maksimainen2010</cite>.

Additionally, Maksimainen et al. have described conformational changes in two loop regions of the active site of Tr-β-gal, thus implicating a conformational selection mechanism for the enzyme. The acid/base catalyst Glu200 exhibited two different conformations which affect the p''K''<sub>a</sub> value of this residue and thus the catalytic mechanism.

== Family Firsts ==
;First stereochemistry determination:
Human β-galactosidase precursor by NMR <cite>Zhang1994</cite>

;First catalytic nucleophile identification:
Human β-galactosidase precursor by 2-fluorogalactose labeling <cite>McCarter1997</cite>.

;First general acid/base residue identification:
''Penicillium sp.'' β-galactosidase by structural identification <cite>Rojas2004</cite>.

;First 3-D structure:
''Penicillium sp.'' β-galactosidase <cite>Rojas2004</cite>.

== References ==
<biblio>
#Ahn2007 pmid=17466346
#Smith2000 pmid=10889266
#Lazan2004 pmid=15694277
#Ross1994 pmid=7991682
#Tanthanuch2008 pmid=18664295
#Tanka2003 pmid=12923090
#Liu2006 pmid=16912928
#Zhang1994 pmid=7998946
#Henrissat1995 pmid=7624375
#McCarter1997 pmid=8995274
#Rojas2004 pmid=15491613
#Blanchard2001 pmid=11423106
#Maksimainen2010 Maksimainen M, Hakulinen N, Kallio JM, Timoharju T, Turunen O, Rouvinen J. ''Crystal structures of Trichoderma reesei beta-galactosidase reveal conformational changes in the active site.'' J Struct Biol. 2010, ''in press.'' //''Note: Due to a problem with PubMed data, this reference is not automatically formatted. Please see these links out:'' [http://dx.doi.org/10.1016/j.jsb.2010.11.024 DOI:10.1016/j.jsb.2010.11.024] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21130883 PMID:21130883]
#GeislerLee2006 pmid=16415215
#Henrissat2001 pmid=11554480
#Tuskan2006 pmid=16973872
#Gamauf2007 pmid=17381511
#Zinin2002 pmid=11909597
#van Casteren2000 pmid=11086688
#Wang2009 pmid=19453169
#Kotake2005 pmid=15980190
</biblio>

[[Category:Glycoside Hydrolase Families|GH035]]

Glycoside Hydrolase Family 35

2011-02-03T14:48:14Z

Anna Kulminskaya:

{{UnderConstruction}}
* [[Author]]s: ^^^Alexander Golubev^^^ and ^^^Anna Kulminskaya^^^
* [[Responsible Curator]]: ^^^Anna Kulminskaya^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH35'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH35.html
|}
</div>


== Substrate specificities ==
The major activity of enzymes of this GH family is β-galactosidase (EC 3.2.1.23). Reported enzymes were isolated from microorganisms such as fungi, bacteria and yeasts; plants, animals and human cells, and from recombinant sources and act in acidic conditions. The β-galactosidase (EC 3.2.1.23) catalyses the hydrolysis of terminal non-reducing β-D-galactose residues in β-D-galactosides as, for example, lactose (1,4-O-β-D-galactopyranosyl-D-glucose) and structurally related compounds. GH35 includes multiple genes in various plant species <cite>Ahn2007, Smith2000, Lazan2004, Ross1994, Tanthanuch2008</cite> suggesting ubiquity of GH35 gene multiplicity in plants. Family 35 β-galactosidases demonstrate specificity towards β1,3-, β1,6- or β1,4-galactosidic linkages. Plant β-galactosidases can be divided into two classes: members of the first are capable of hydrolyzing pectic β-1,4-galactans; another ones can specifically cleave β-1,3- and β1,6-galactosyl linkages of arabinogalactan proteins.

Besides β-galactosidases, GHF35 contains two exo-β-glucosaminidases (EC 3.2.1.165) <cite>Fukui2005</cite>, <cite>Kawarabayasi1998</cite>. This enzyme hydrolyze chitosan or chitosan oligosaccharides to remove successive D-glucosamine residues from the non-reducing termini.

== Kinetics and Mechanism ==
Beta-galactosidases of GH35 family catalyze hydrolysis of β-galactosyl linkages between terminal galactosyl residues of oligosaccharides, glycolipids, and glycoproteins acting via a double-displacement mechanism and retaining β-anomeric configuration of the released galactose molecule. The stereochemistry of the reaction has been first shown by NMR for human β-galactosidase precursor <cite>Zhang1994</cite> and then confirmed by other investigators for microbial and plant enzymes.

== Catalytic Residues ==
The catalytic residues for family 35 were first predicted on the basis of hydrophobic cluster analysis of proteins of similar protein fold <cite>Henrissat1995</cite>. Experimentally, the glutamic acid residue 268 was first identified as the catalytic nucleophile in human lysosomal β-galactosidase precursor using the slow substrate 2,4-dinitrophenyl-2-deoxy-2-fluoro- β-D-galactopyranoside that trapped a glycosyl enzyme intermediate. It allowed subsequent peptide mapping and exact nulceophile ID <cite>McCarter</cite>. Further, the same work was done for two bacterial β-galactosidases, from Xanthomonas manihotis and Bacillus circulans <cite>Blanchard2001</cite>. The general acid/base catalyst was inferred by structural studies of Penicillium β-galactosidase as Glu200 <cite>Rojas2004</cite>. Recent structural studies of Maksimainen et al. <cite>Maksimainen2010</cite> revealed two different conformations of the general acid/base catalyst Glu200 in the β-galactosidase of Trichoderma reeesei, which influence the catalytic machinery of the enzyme.

== Three-dimensional structures ==
To date, there are only three enzymes from GH family 35 are structurally characterized. First 3D-structure has appeared available at PDB for the β-galactosidase from Pencillium sp. (Psp-β-gal, PDB code1tg7) by Rojas et al. <cite>Rojas2004</cite>. The crystallographic structures of Psp-β-gal and its complex with galactose (PDB code 1xc6) were solved at 1.90 Å and 2.10 Å, respectively. The structure of β-galactosidase from Bacteriodes thetaiotamicron was reported by the New York Structural GenomiX Research Consortium in 2008. In 2010, the crystal structure of Trichoderma reesei (Hypocrea jecorina) β-galactosidase (Tr-β-gal, PDB code 3OG2) at a 1.20 Å resolution and its complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4 Å resolutions, respectively, were reported (PDB codes 3OGR, 3OGS, and 3OGV) by Maksimainen et al. <cite>Maksimainen2010</cite>. Like β-galactosidases from other families, they belong to GH-A super-family, which usually have an (α/β)8 TIM barrel as a catalytic domain. The structural analysis of the galactose-binding site was based on the comparison of the crystallographic models of the native Psp-β-gal and Tr-β-gal and their complexes with galactose. A single galactose molecule is bound to the TIM barrel domain of the enzyme in the chair conformation with its O1 in the β-anomer configuration. Two glutamic acid residues act as proton donor and nucleophile and emanate from strands 4 and 7 of the barrel. Both crystal structures, Psp-β-gal and Tr-β-gal, are similar. However, interpretation of Maksimainen et al. of the structure of Tr-β-gal is a bit different from that presented earlier for Psp-β-gal. Rojas et al considered Psp-β-gal to be divided into five domains combining the second and the third domain, although they form separate sub-units in the structure. So, it was concluded that Tr-β-gal structure contains a central catalytic α/β-barrel surrounded by a horseshoe consisting of five ant-parallel β-sandwich structures.

Additionally, Maksimainen et al. described conformational changes in the two loop regions in the active site of Tr-β-gal, implicating a conformational selection-mechanism for the enzyme. An acid/base catalyst Glu200 showed two different conformations which affect pKa value of this residue and the catalytic mechanism.

== Family Firsts ==
;First stereochemistry determination:
Human β-galactosidase precursor by NMR <cite>Zhang1994</cite>

;First catalytic nucleophile identification:
Human β-galactosidase precursor by 2-fluorogalactose labeling <cite>McCarter1997</cite>.

;First general acid/base residue identification:
Penicillium sp. β-galactosidase by structural identification <cite>Rojas2004</cite>.

;First 3-D structure:
Penicillium β-galactosidase <cite>Rojas2004</cite>.

== References ==
<biblio>
#Ahn2007 pmid=17466346
#Smith2000 pmid=10889266
#Lazan2004 pmid=15694277
#Ross1994 pmid=7991682
#Tanthanuch2008 pmid=18664295
#Fukui2005 pmid=15710748
#Kawarabayasi1998 pmid=9679203
#Zhang1994 pmid=7998946
#Henrissat1995 pmid=7624375
#McCarter1997 pmid=8995274
#Rojas2004 pmid=15491613
#Blanchard2001 pmid=11423106
#Maksimainen2010 Maksimainen M, Hakulinen N, Kallio JM, Timoharju T, Turunen O, Rouvinen J. ''Crystal structures of Trichoderma reesei beta-galactosidase reveal conformational changes in the active site.'' J Struct Biol. 2010, ''in press.'' //''Note: Due to a problem with PubMed data, this reference is not automatically formatted. Please see these links out:'' [http://dx.doi.org/10.1016/j.jsb.2010.11.024 DOI:10.1016/j.jsb.2010.11.024] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21130883 PMID:21130883]

</biblio>

[[Category:Glycoside Hydrolase Families|GH035]]

Glycoside Hydrolase Family 35

2011-02-03T13:30:42Z

Anna Kulminskaya:

{{UnderConstruction}}
* [[Author]]s: ^^^Alexander Golubev^^^ and ^^^Anna Kulminskaya^^^
* [[Responsible Curator]]: ^^^Anna Kulminskaya^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH35'''
|-
|'''Clan'''
|GH-A
|-
|'''Mechanism'''
|retaining
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}GH35.html
|}
</div>


== Substrate specificities ==
The major activity of enzymes of this GH family is β-galactosidase (EC 3.2.1.23). Reported enzymes were isolated from microorganisms such as fungi, bacteria and yeasts; plants, animals and human cells, and from recombinant sources and act in acidic conditions. The β-galactosidase (EC 3.2.1.23) catalyses the hydrolysis of terminal non-reducing β-D-galactose residues in β-D-galactosides as, for example, lactose (1,4-O-β-D-galactopyranosyl-D-glucose) and structurally related compounds. GH35 includes multiple genes in various plant species <cite>Ahn2007, Smith2000, Lazan2004, Ross1994, Tanthanuch2008</cite> suggesting ubiquity of GH35 gene multiplicity in plants. Family 35 β-galactosidases demonstrate specificity towards β1,3-, β1,6- or β1,4-galactosidic linkages. Plant β-galactosidases can be divided into two classes: members of the first are capable of hydrolyzing pectic β-1,4-galactans; another ones can specifically cleave β-1,3- and β1,6-galactosyl linkages of arabinogalactan proteins.

Besides β-galactosidases, GHF35 contains two exo-β-glucosaminidases (EC 3.2.1.165) <cite>Fukui2005</cite>, <cite>Kawarabayasi1998</cite>. This enzyme hydrolyze chitosan or chitosan oligosaccharides to remove successive D-glucosamine residues from the non-reducing termini.

== Kinetics and Mechanism ==
Beta-galactosidases of GH35 family catalyze hydrolysis of β-galactosyl linkages between terminal galactosyl residues of oligosaccharides, glycolipids, and glycoproteins acting via a double-displacement mechanism and retaining β-anomeric configuration of the released galactose molecule. The stereochemistry of the reaction has been first shown by NMR for human β-galactosidase precursor <cite>Zhang1994</cite> and then confirmed by other investigators for microbial and plant enzymes.

== Catalytic Residues ==
The catalytic residues for family 35 were first predicted on the basis of hydrophobic cluster analysis of proteins of similar protein fold <cite>Henrissat1995</cite>. Experimentally, the glutamic acid residue 268 was first identified as the catalytic nucleophile in human lysosomal β-galactosidase precursor using the slow substrate 2,4-dinitrophenyl-2-deoxy-2-fluoro- β-D-galactopyranoside that trapped a glycosyl enzyme intermediate. It allowed subsequent peptide mapping and exact nulceophile ID <cite>McCarter</cite>. Further, the same work was done for two bacterial β-galactosidases, from Xanthomonas manihotis and Bacillus circulans <cite>Blanchard2001</cite>. The general acid/base catalyst was inferred by structural studies of Penicillium β-galactosidase as Glu200 <cite>Rojas2004</cite>. Recent structural studies of Maksimainen et al. <cite>Maksimainen2010</cite> revealed two different conformations of the general acid/base catalyst Glu200 in the β-galactosidase of Trichoderma reeesei, which influence the catalytic machinery of the enzyme.

== Three-dimensional structures ==
To date, there are only three enzymes from GH family 35 are structurally characterized. First 3D-structure has appeared available at PDB for the β-galactosidase from Pencillium sp. (Psp-β-gal, PDB by Rojas et al. (2004). The crystallographic structures of Psp-β-gal and its complex with galactose were solved at 1.90 Å and 2.10 Å, respectively. The structure of β-galactosidase from Bacteriodes thetaiotamicron was reported by the New York Structural GenomiX Research Consortium in 2008. In 2010, the crystal structure of Trichoderma reesei (Hypocrea jecorina) β-galactosidase (Tr-β-gal) at a 1.20 Å resolution and its complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4 Å resolutions, respectively, were reported. Like β-galactosidases from other families, they belong to GH-A super-family, which usually have an (α/β)8 TIM barrel as a catalytic domain. The structural analysis of the galactose-binding site was based on the comparison of the crystallographic models of the native Psp-β-gal and Tr-β-gal and their complexes with galactose. A single galactose molecule is bound to the TIM barrel domain of the enzyme in the chair conformation with its O1 in the β-anomer configuration. Two glutamic acid residues act as proton donor and nucleophile and emanate from strands 4 and 7 of the barrel. Both crystal structures, Psp-β-gal and Tr-β-gal, are similar. However, interpretation of Maksimainen et al. of the structure of Tr-β-gal is a bit different from that presented earlier for Psp-β-gal. Rojas et al considered Psp-β-gal to be divided into five domains combining the second and the third domain, although they form separate sub-units in the structure. So, it was concluded that Tr-β-gal structure contains a central catalytic α/β-barrel surrounded by a horseshoe consisting of five ant-parallel β-sandwich structures.

Additionally, Maksimainen et al. described conformational changes in the two loop regions in the active site of Tr-β-gal, implicating a conformational selection-mechanism for the enzyme. An acid/base catalyst Glu200 showed two different conformations which affect pKa value of this residue and the catalytic mechanism.

== Family Firsts ==
;First stereochemistry determination:
Human β-galactosidase precursor by NMR <cite>Zhang1994</cite>

;First catalytic nucleophile identification:
Human β-galactosidase precursor by 2-fluorogalactose labeling <cite>McCarter1997</cite>.

;First general acid/base residue identification:
Penicillium sp. β-galactosidase by structural identification <cite>Rojas2004</cite>.

;First 3-D structure:
Penicillium β-galactosidase <cite>Rojas2004</cite>.

== References ==
<biblio>
#Ahn2007 pmid=17466346
#Smith2000 pmid=10889266
#Lazan2004 pmid=15694277
#Ross1994 pmid=7991682
#Tanthanuch2008 pmid=18664295
#Fukui2005 pmid=15710748
#Kawarabayasi1998 pmid=9679203
#Zhang1994 pmid=7998946
#Henrissat1995 pmid=7624375
#McCarter1997 pmid=8995274
#Rojas2004 pmid=15491613
#Blanchard2001 pmid=11423106
#Maksimainen2010 Maksimainen M, Hakulinen N, Kallio JM, Timoharju T, Turunen O, Rouvinen J. ''Crystal structures of Trichoderma reesei beta-galactosidase reveal conformational changes in the active site.'' J Struct Biol. 2010, ''in press.'' //''Note: Due to a problem with PubMed data, this reference is not automatically formatted. Please see these links out:'' [http://dx.doi.org/10.1016/j.jsb.2010.11.024 DOI:10.1016/j.jsb.2010.11.024] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=21130883 PMID:21130883]

</biblio>

[[Category:Glycoside Hydrolase Families|GH035]]

Glycoside Hydrolase Family 35

2011-01-31T10:09:44Z

Anna Kulminskaya:

Glycoside Hydrolase Family 35

2011-01-31T10:07:38Z

Anna Kulminskaya:

Glycoside Hydrolase Family 35

2011-01-31T09:30:31Z

Anna Kulminskaya:

Glycoside Hydrolase Family 35

2011-01-31T08:35:55Z

Anna Kulminskaya:

Glycoside Hydrolase Family 35

2011-01-28T13:59:29Z

Anna Kulminskaya:

Glycoside Hydrolase Family 35

2011-01-28T13:42:34Z

Anna Kulminskaya:

User:Anna Kulminskaya

2010-10-06T09:13:28Z

Anna Kulminskaya:

I’m a research scientist at the Petersburg Nuclear Physics Institute, Molecular and Radiation Biophysics Department, Russia. I received my PhD degree under supervision of Neustroev Kirill studying the exo-inulinase from Aspergillus awamori (GH32). Now I’m a leader of the Laboratory of Enzymology at the same Institute.

The main Research area of our team is carbohydrate enzymology and applications. We focus in understanding the way in which particular enzymes act to alter the structure of poly- or oligosaccharides found in Nature, and to harness these enzymes for practical applications. Using the tools of chemo-organic synthesis and biochemistry, our work aims to provide increased understanding of the chemical principles underlying mechanisms of action of glycoside hydrolases with transglycosylating activity.

We are particularly interested in the alpha-galactosidases (GH27 and 36), beta-galactosidase (GH35), beta-xylosidases (GH3), beta-xylanases, cellulose-degrading enzymes, alpha- or beta-mannosidases (GH2) and alpha-L-fucosidases.

[[Category:Contributors|Kulminskaya,Anna]]

Glycoside Hydrolase Family 35

2010-10-04T11:12:09Z

Anna Kulminskaya:

Glycoside Hydrolase Family 35

2010-10-04T10:23:00Z

Anna Kulminskaya:

Glycoside Hydrolase Family 35

2010-10-04T10:16:01Z

Anna Kulminskaya:

Glycoside Hydrolase Family 35

2010-09-16T08:59:31Z

Anna Kulminskaya:

User:Anna Kulminskaya

2010-09-16T08:50:51Z

Anna Kulminskaya: Blanked the page

User:Anna Kulminskaya

2010-09-16T08:49:39Z

Anna Kulminskaya: Created page with "Hi, I'm Anna Kulminskaya."

Hi, I'm Anna Kulminskaya.