CAZypedia - User contributions [en-ca]

User:Richard McLean

2014-09-11T20:34:33Z

Richard McLean:

[[Image:richard.mclean.jpg|200px|right]]

I received a BSc in Biochemistry in 2013 from the University of Lethbridge and am currently working towards a MSc. I have been working at the Lethbridge Research Center under Dr. ^^^Wade Abbott^^^ since 2012. My research has focused predominantly on using kinetics, chromatography, mutagenesis, and crystallography to work out structure function differences between subfamily 1 and 2 of the Family 2 Lyases. I have also worked to a lesser extent on PL22s and a mannose-6-monophosphatase.
----


[[Category:Contributors|McLean,Richard]]

File:Richard.mclean.jpg

2014-09-11T19:30:52Z

Richard McLean:

Polysaccharide Lyase Family 22

2014-09-10T16:14:17Z

Richard McLean:

{{UnderConstruction}}
* [[Author]]: ^^^Richard McLean^^^ and ^^^Wade Abbott^^^
* [[Responsible Curator]]: ^^^Wade Abbott^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL22'''
|-
|'''3D Structure'''
|β<sub>7</sub> propeller
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|manganese
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL22.html
|}
</div>


== Substrate specificities ==
Family 22 Polysaccharide Lyases (PL22s) contain two subfamilies and several outlier sequences <cite>Lombard2010</cite>. Originally referred to as oligogalacturonide transeliminases (OGTE)<cite>Moran1968</cite>, PL22s are now commonly referred to as oligogalacturonide lyases (OGLs).

As the name suggests, PL22s remove 5-keto-4-deoxyuronate (4-deoxy-{{smallcaps|l}}-threo-5-hexosulose uronic acid, DKI) from short chain oligalacturonides and display preferential activity on digalacturonate and Δ4,5-unsaturated digalacturonate <cite>Abbott2010</cite><cite>Kester1999</cite>. Activity on trigalacturonate is significantly lower and PL22s appear to lack activity on long chain polymers of α-(1,4)-linked polygalacturonate altogether <cite>Abbott2010</cite><cite>Kester1999</cite>. Differing levels of activity has been reported on methylated short chain oligogalacturonides depending on the location of methylation <cite>Kester1999</cite>.

== Kinetics and Mechanism ==
PL22s harness a β-elimination reaction to cleave the glycosidic bonds in oligogalacturonides, similar to other pectate lyases. This process requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn2+ or Mg2+) for acidification of the α-proton and charge neutralization. YePL22 (YE1876 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081; [http://www.ncbi.nlm.nih.gov/protein/123442156 gi|123442156|]) displays the lowest reported pH optimum for a pectate lyase (7.3 - 7.7) <cite>Abbott2010</cite>, which is substantially lower than other families that deploy catalytic arginines or lysines in the β-elimination of pectate.

== Catalytic Residues ==
Within the structure of YePL22 H242 is the only basic residue that is in proximity of the α-proton of a modelled galacturonate <cite>Abbott2010</cite>. This histidine is highly conserved within PL22s with only ''Candidatus Solibacter usitatus'' Ellin6076 ([http://www.ncbi.nlm.nih.gov/protein/116225114 gi|116225114|]) displaying an alternative residue (T236); however, whether this gene product is a lyase has yet to be determined. The stabilizing base (YE1876: R217) is completely conserved across the PL22 family.

The metal coordination pocket houses a manganese ion and is comprised of three histidines (VPA0088: H287, H353, H355; YE1876: H287, H353, H355) and one glutamine (VPA0088: Q350; YeOGL: Q350). It is of note however that although these residues are perfectly conserved in all reported subfamily 1 sequences and several outlier sequences, there are minor differences in subfamily 2 sequences <cite>Lombard2010</cite>. In subfamily 2, H287 is invariant; however, Q350 is not conserved, and H353 and H355 have been replaced with a glutamate and asparagine respectively. These modifications may alter the chemistry of metal coordination selectivity. Further experimentation will be required to define this relationship.

== Three-dimensional structures ==
[[Image:3pe7.png|thumb|230px|YePL22 in complex with Mn<sup>2+</sup> and acetate]]The first structure of a PL22 determined was ''Vibrio parahaemolyticus'' RIMD 2210633 ([{{PDBlink}}3c5m PDB 3C5M]) solved in 2008 by x-ray diffraction to 2.60 Å ([http://www.nesg.org/ Northeast Structural Genomics Consortium]). This was followed in 2010 by ''Yersinia enterocolitica'' subsp. enterocolitica 8081 ([{{PDBlink}}3pe7 PDB 3PE7]), which was solved in complex with Mn<sup>2+</sup> and acetate by x-ray diffraction to 1.65 Å. The two proteins share ~69% sequence identity and highly similar 3D structures. The PL22 fold is a β<sub>7</sub> propeller with the catalytic machinery and metal coordination pocket housed at the center of the enzyme.

== Family Firsts ==
;First catalytic activity: OGTE from ''Pectobacterium carotovorum'' ICPB EC153 (previously ''Erwinia carotovora''). <cite>Moran1968</cite>
;First catalytic base identification: YeOGL (YE1876) H242 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081. <cite>Abbott2010</cite>
;First catalytic divalent cation identification: OGL (Dda3937_03686) from ''Dickeya Dadantii'' 3937 (previously ''Erwinia chrysanthemi'' 3937). <cite>Shevchik1989</cite>.
;First 3-D structure: VPA0088 from ''Vibrio parahaemolyticus'' RIMD 2210633. ([{{PDBlink}}3c5m PDB 3C5M])

== References ==
<biblio>
#Abbott2010 pmid=20851883
#Collmer1981 pmid=16593039
#Kester1999 pmid=10601263
#Moran1968 pmid=5671040
#Reverchon1987 pmid=3623103
#Reverchon1989 pmid=2695393
#Shevchik1989 pmid=10383957
#Yang2007 pmid=17189441
#Lombard2010 pmid=20925655
</biblio>

[[Category:Polysaccharide Lyase Families|PL022]]

Polysaccharide Lyase Family 22

2014-09-08T16:40:25Z

Richard McLean:

{{UnderConstruction}}
* [[Author]]: ^^^Richard McLean^^^ and ^^^Wade Abbott^^^
* [[Responsible Curator]]: ^^^Wade Abbott^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL22'''
|-
|'''3D Structure'''
|β<sub>7</sub> propeller
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|manganese
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL22.html
|}
</div>


== Substrate specificities ==
Family 22 lyases of CAZy contain two subfamilies <cite>Lombard2010</cite> and several outlier sequences. Originally referred to as oligogalacturonide trans-eliminases (OGTE)<cite>Moran1968</cite>, Family 22 lyases are now commonly referred to as oligogalacturonide lyases (OGLs).

As the name suggests, OGLs are typically preferentially active on short chain oligomers of galacturonides. Several studies have been undertaken to evaluate the specificity of PL22s, and have found that optimal activity is seen with digalacturonate and Δ4,5-unsaturated digalacturonate <cite>Abbott2010</cite><cite>Kester1999</cite>. Activity on trigalacturonate has been shown to be significantly lower than that on digalacturonate and although activity on the unsaturated dimer was lower than that of the saturated dimer, activity on Δ4,5-unsaturated trigalacturonate is comparable or higher than that of saturated trigalacturonate <cite>Kester1999</cite>. No assays on larger oligomers have been reported at this time however, OGLs lack activity on long chain polymers of α-(1,4)-linked polygalacturonate.

Activity has been demonstrated on methylated short chain galacturonides with differing levels of activity depending on the location of methylation <cite>Kester1999</cite>. Activity on 1-methyl digalacturonate was only half of what was seen on digalacturonate and no activity was found on 2-methyl digalacturonate. A similar trend was shown on trigalacturonate as well with roughly half the activity on 1-methyl trigalacturonate as on trigalacturonate and no activity on 2-methyl galacturonate. Interestingly though, nearly triple activity was seen on 3-methyl galacturonate as on unmethylated trigalacturonate.

== Kinetics and Mechanism ==

== Catalytic Residues ==
The Brønstead base for Family 22 lyases is a histidine. <cite>Abbott2010</cite> H242 in YE1876 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081 was the first and is to date, the only catalytic residue determined in a Family 22 lyase. This histidine is nearly perfectly conserved within Family 22 lyases reported in the CAZy database with a single exception, that of ''Candidatus Solibacter usitatus'' Ellin6076 ([http://www.ncbi.nlm.nih.gov/protein/116225114 gi|116225114|]) in which the histidine has been mutated to threonine T236.

The metal coordination pocket houses a manganese ion and is comprised of three histidines (VPA0088 H287, H353, H355; YeOGL H287, H353, H355) and one glutamine (VPA0088 Q350; YeOGL Q350). It is of note however, that although these residues are perfectly conserved in all reported subfamily 1 and several outlier sequences, this is not the case for subfamily 2 or archaeal sequences. The three archaeal sequences have similar histidines but the Q350 has been replaced in two cases with an aspartate and in one case, no residue has identity. In subfamily 2, there is a histidine in place of H287 however there is no residue identity with Q350 and H353 and H355 have been replaced with a glutamate and asparagine respectively. These modifications may result in a substantially different metal coordination pocket.

== Three-dimensional structures ==
[[Image:3C5M.jpg|thumb|230px|A 7-bladed β-propeller]]The first structure of a Family 22 Lyase was the ''Vibrio parahaemolyticus'' RIMD 2210633 PDBID: 3C5M fused to a c-terminal polyhistidine tag and was solved in 2008 by x-ray diffraction to 2.60 Å. This was followed in 2010 by ''Yersinia enterocolitica'' subsp. enterocolitica 8081 PDBID: 3PE7 which lacked any fusions and was also solved by x-ray diffraction to 1.65 Å. The two proteins share 68.81% sequence identity and highly similar 3D structures.

== Family Firsts ==
;First catalytic activity: OGTE from ''Pectobacterium carotovorum'' ICPB EC153 (previously ''Erwinia carotovora''). <cite>Moran1968</cite>
;First catalytic base identification: YeOGL (YE1876) H242 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081. <cite>Abbott2010</cite>
;First catalytic divalent cation identification: OGL (Dda3937_03686) from ''Dickeya Dadantii'' 3937 (previously ''Erwinia chrysanthemi'' 3937). <cite>Shevchik1989</cite>.
;First 3-D structure: VPA0088 from ''Vibrio parahaemolyticus'' RIMD 2210633. ([{{PDBlink}}3C5M PDB 3C5M])

== References ==
<biblio>
#Abbott2010 pmid=20851883
#Collmer1981 pmid=16593039
#Kester1999 pmid=10601263
#Moran1968 pmid=5671040
#Reverchon1987 pmid=3623103
#Reverchon1989 pmid=2695393
#Shevchik1989 pmid=10383957
#Yang2007 pmid=17189441
#Lombard2010 pmid=20925655
</biblio>

[[Category:Polysaccharide Lyase Families|PL022]]

File:3C5M.jpg

2014-09-07T22:08:01Z

Richard McLean:

Polysaccharide Lyase Family 22

2014-09-05T21:08:45Z

Richard McLean:

{{UnderConstruction}}
* [[Author]]: ^^^Richard McLean^^^ and ^^^Wade Abbott^^^
* [[Responsible Curator]]: ^^^Wade Abbott^^^
----


<div style="float:right">
{| {{Prettytable}}
|-
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL22'''
|-
|'''3D Structure'''
|β-<sub>7</sub> propeller
|-
|'''Mechanism'''
|β-elimination
|-
|'''Charge neutraliser'''
|manganese
|-
|'''Active site residues'''
|known
|-
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
|-
| colspan="2" |{{CAZyDBlink}}PL22.html
|}
</div>


== Substrate specificities ==
Family 22 lyases of CAZy contain two subfamilies, several outlier sequences, and three archaeal sequences. Originally referred to as oligogalacturonide trans-eliminases (OGTE)<cite>Moran1968</cite>, Family 22 lyases are now commonly referred to as oligogalacturonide lyases (OGL).

As the name suggests, OGLs are typically preferentially active on short chain oligomers of galacturonides. Several studies have been undertaken to evaluate the flexibility of the active site of OGL and have found that optimal activity is seen with digalacturonate and Δ4,5-unsaturated digalacturonate. <cite>Abbott2010</cite><cite>Kester1999</cite> Activity on trigalacturonate has been shown to be significantly lower than that on digalacturonate and although activity on the unsaturated dimer was lower than that of the saturated dimer, activity on Δ4,5-unsaturated trigalacturonate is comparable or higher than that of saturated trigalacturonate. <cite>Kester1999</cite> No assays on larger oligomers have been reported at this time however, OGLs lack activity on long chain polymers of α-(1,4)-linked polygalacturonate.

Activity has been demonstrated on methylated short chain galacturonides with differing levels of activity depending on the location of methylation. <cite>Kester1999</cite> Activity on 1-methyl digalacturonate was only half of what was seen on digalacturonate and no activity was found on 2-methyl digalacturonate. A similar trend was shown on trigalacturonate as well with roughly half the activity on 1-methyl trigalacturonate as on trigalacturonate and no activity on 2-methyl galacturonate. Interestingly though, nearly triple activity was seen on 3-methyl galacturonate as on unmethylated trigalacturonate.

== Kinetics and Mechanism ==

== Catalytic Residues ==
The Brønstead base for Family 22 lyases is a histidine. <cite>Abbott2010</cite> H242 in YE1876 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081 was the first and is to date, the only catalytic residue determined in a Family 22 lyase. This histidine is nearly perfectly conserved within Family 22 lyases reported in the CAZy database with a single exception, that of ''Candidatus Solibacter usitatus'' Ellin6076 ([http://www.ncbi.nlm.nih.gov/protein/116225114 gi|116225114|]) in which the histidine has been mutated to threonine T236.

The metal coordination pocket houses a manganese ion and is comprised of three histidines (VPA0088 H287, H353, H355; YeOGL H287, H353, H355) and one glutamine (VPA0088 Q350; YeOGL Q350). It is of note however, that although these residues are perfectly conserved in all reported subfamily 1 and several outlier sequences, this is not the case for subfamily 2 or archaeal sequences. The three archaeal sequences have similar histidines but the Q350 has been replaced in two cases with an aspartate and in one case, no residue has identity. In subfamily 2, there is a histidine in place of H287 however there is no residue identity with Q350 and H353 and H355 have been replaced with a glutamate and asparagine respectively. These modifications may result in a substantially different metal coordination pocket.

== Three-dimensional structures ==

== Family Firsts ==
;First catalytic activity: OGTE from ''Pectobacterium carotovorum'' ICPB EC153 (previously ''Erwinia carotovora''). <cite>Moran1968</cite>
;First catalytic base identification: YeOGL (YE1876) H242 from ''Yersinia enterocolitica'' subsp. enterocolitica 8081. <cite>Abbott2010</cite>
;First catalytic divalent cation identification: OGL (Dda3937_03686) from ''Dickeya Dadantii'' 3937 (previously ''Erwinia chrysanthemi'' 3937). <cite>Shevchik1989</cite>.
;First 3-D structure: VPA0088 from ''Vibrio parahaemolyticus'' RIMD 2210633. ([{{PDBlink}}3C5M PDB 3C5M])

== References ==
<biblio>
#Abbott2010 pmid=20851883
#Collmer1981 pmid=16593039
#Kester1999 pmid=10601263
#Moran1968 pmid=5671040
#Reverchon1987 pmid=3623103
#Reverchon1989 pmid=2695393
#Shevchik1989 pmid=10383957
#Yang2007 pmid=17189441
</biblio>

[[Category:Polysaccharide Lyase Families|PL022]]

Polysaccharide Lyase Family 22

2014-09-05T17:56:25Z

Richard McLean: