https://www.cazypedia.org/api.php?action=feedcontributions&user=Leila+LoLeggio&feedformat=atomCAZypedia - User contributions [en-ca]2024-03-29T01:19:58ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_53&diff=10633Glycoside Hydrolase Family 532015-05-29T16:41:29Z<p>Leila LoLeggio: /* Function and Substrate specificities */</p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Leila Lo Leggio^^^<br />
* [[Responsible Curator]]: ^^^Leila Lo Leggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH53'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH53.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Function and Substrate specificities ==<br />
The only known specificity for [[glycoside hydrolase]]s of this family is &beta;-1,4-galactanase (EC [{{EClink}}3.2.1.89 3.2.1.89]) and the only reported function is the microbial degradation of galactans and arabinogalactans in the pectic component of plant cell walls. A number of patents on industrial applications of GH53 have been filed. In a number of bacteria, GH53 &beta;-1,4-galactanases genes have been found as part of gene clusters devoted to galactan utilization and additionally comprising genes encoding for a GH42 &beta;-1,4-galactosidase, a galactooligosaccharide transport system and a transcriptional regulator.<br />
<br />
== Kinetics and Mechanism ==<br />
GH53 &beta;-1,4-galactanases follow a [[retaining]] mechanism as first demonstrated by following the stereochemical course of rection for the [[endo]]-&beta;-1,4-galactanase of the bacterium ''Cellvibrio japonicus'' (at that time referred to as ''Pseudomonas fluorescens'' subspecies ''cellulosa'') <cite>Braithwaite1997</cite>. Most characterized members have been reported to be [[endo]]-acting, although processivity has been suggested in one case <cite>Hinz2005</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were first identified for the [[endo]]-&beta;-1,4-galactanase of the bacterium ''Cellvibrio japonicus'' <cite>Braithwaite1997</cite> (previously known as ''Pseudomonas fluorescens'' subspecies ''cellulosa''). Prior to structure determination Henrissat used hydrophobic cluster analysis and sequence alignments to predict that the family belonged to clan GH-A, and the two proposed catalytic residues, which were confirmed by a combination of mutagenesis and kinetic analysis; one acting as a [[general acid/base]] (E161) and the other as a [[catalytic nucleophile]] (E270).<br />
<br />
== Three-dimensional structures ==<br />
As for all members of Clan GH-A <cite>Jenkins1995, Henrissat1995</cite>, structurally characterized GH53 enzymes <cite>Ryttersgaard2002,LeNours2003,Ryttersgaard2004</cite> display a (&beta;/&alpha;)<sub>8</sub> barrel structure for the catalytic domain, usually with fairly compact loop structure and a sequence under 400 residues in length. The catalytic residues are typically positioned at the C-terminal ends of &beta;strands 4 and 7 in the barrel. Somewhat unusually, none of the four structurally characterized GH53 catalytic domains was accompanied by other catalytic domains or accessory modules, but modularity can be inferred by sequence in other members of the family. A disulphide bridging two loops (&beta;/&alpha; loops 7 and 8) in 3 known fungal structures <cite>Ryttersgaard2002,LeNours2003</cite>, is replaced functionally by a calcium ion in one bacterial structure <cite>Ryttersgaard2004</cite>. For one bacterial member of the family ligand complexes with products have been obtained crystallographically, occupying subsites -4 to -2 and +1 to +2 <cite>Ryttersgaard2004,LeNours2009</cite>. Based on these crystal structures, binding of a galactononaose fragment has also been computationally modelled <cite>LeNours2009</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Cellvibrio japonicus'' endo-&beta;-1,4-galactanase <cite>Braithwaite1997</cite>.<br />
;First [[catalytic nucleophile]] identification: ''Cellvibrio japonicus'' endo-&beta;-1,4-galactanase <cite>Braithwaite1997</cite>.<br />
;First [[general acid/base]] residue identification: ''Cellvibrio japonicus'' endo-&beta;-1,4-galactanase <cite>Braithwaite1997</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' endo-&beta;-1,4-galactanase <cite>Ryttersgaard2002</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Braithwaite1997 pmid=9398278<br />
#Hinz2005 pmid=16151143<br />
#Jenkins1995 pmid=7729513<br />
#Henrissat1995 pmid=7624375<br />
#Ryttersgaard2002 pmid=12484750<br />
#LeNours2003 pmid=12761390<br />
#Ryttersgaard2004 pmid=15312766<br />
#LeNours2009 pmid=19089956<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH053]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_53&diff=10632Glycoside Hydrolase Family 532015-05-29T16:33:37Z<p>Leila LoLeggio: /* Substrate specificities */</p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Leila Lo Leggio^^^<br />
* [[Responsible Curator]]: ^^^Leila Lo Leggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH53'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH53.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Function and Substrate specificities ==<br />
The only known specificity for [[glycoside hydrolase]]s of this family is &beta;-1,4-galactanase (EC [{{EClink}}3.2.1.89 3.2.1.89]) and the only reported function is the microbial degradation of galactans and arabinogalactans in the pectic component of plant cell walls. A number of patents on industrial applications of GH53 have been filed.In a number of bacteria, GH53 &beta;-1,4-galactanases genes have been found as part of gene clusters devoted to galactan utilization and additionally comprising genes encoding for a GH42 &beta;-1,4-galactosidase, a galactooligosaccharide transport system and a transcriptional regulator.<br />
<br />
== Kinetics and Mechanism ==<br />
GH53 &beta;-1,4-galactanases follow a [[retaining]] mechanism as first demonstrated by following the stereochemical course of rection for the [[endo]]-&beta;-1,4-galactanase of the bacterium ''Cellvibrio japonicus'' (at that time referred to as ''Pseudomonas fluorescens'' subspecies ''cellulosa'') <cite>Braithwaite1997</cite>. Most characterized members have been reported to be [[endo]]-acting, although processivity has been suggested in one case <cite>Hinz2005</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were first identified for the [[endo]]-&beta;-1,4-galactanase of the bacterium ''Cellvibrio japonicus'' <cite>Braithwaite1997</cite> (previously known as ''Pseudomonas fluorescens'' subspecies ''cellulosa''). Prior to structure determination Henrissat used hydrophobic cluster analysis and sequence alignments to predict that the family belonged to clan GH-A, and the two proposed catalytic residues, which were confirmed by a combination of mutagenesis and kinetic analysis; one acting as a [[general acid/base]] (E161) and the other as a [[catalytic nucleophile]] (E270).<br />
<br />
== Three-dimensional structures ==<br />
As for all members of Clan GH-A <cite>Jenkins1995, Henrissat1995</cite>, structurally characterized GH53 enzymes <cite>Ryttersgaard2002,LeNours2003,Ryttersgaard2004</cite> display a (&beta;/&alpha;)<sub>8</sub> barrel structure for the catalytic domain, usually with fairly compact loop structure and a sequence under 400 residues in length. The catalytic residues are typically positioned at the C-terminal ends of &beta;strands 4 and 7 in the barrel. Somewhat unusually, none of the four structurally characterized GH53 catalytic domains was accompanied by other catalytic domains or accessory modules, but modularity can be inferred by sequence in other members of the family. A disulphide bridging two loops (&beta;/&alpha; loops 7 and 8) in 3 known fungal structures <cite>Ryttersgaard2002,LeNours2003</cite>, is replaced functionally by a calcium ion in one bacterial structure <cite>Ryttersgaard2004</cite>. For one bacterial member of the family ligand complexes with products have been obtained crystallographically, occupying subsites -4 to -2 and +1 to +2 <cite>Ryttersgaard2004,LeNours2009</cite>. Based on these crystal structures, binding of a galactononaose fragment has also been computationally modelled <cite>LeNours2009</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: ''Cellvibrio japonicus'' endo-&beta;-1,4-galactanase <cite>Braithwaite1997</cite>.<br />
;First [[catalytic nucleophile]] identification: ''Cellvibrio japonicus'' endo-&beta;-1,4-galactanase <cite>Braithwaite1997</cite>.<br />
;First [[general acid/base]] residue identification: ''Cellvibrio japonicus'' endo-&beta;-1,4-galactanase <cite>Braithwaite1997</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' endo-&beta;-1,4-galactanase <cite>Ryttersgaard2002</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Braithwaite1997 pmid=9398278<br />
#Hinz2005 pmid=16151143<br />
#Jenkins1995 pmid=7729513<br />
#Henrissat1995 pmid=7624375<br />
#Ryttersgaard2002 pmid=12484750<br />
#LeNours2003 pmid=12761390<br />
#Ryttersgaard2004 pmid=15312766<br />
#LeNours2009 pmid=19089956<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH053]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10302User:Leila LoLeggio2014-09-19T07:00:43Z<p>Leila LoLeggio: </p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily <cite>Jenkins1995</cite>, then to become Clan GH-A<cite>Henrissat1995</cite>.<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
<br />
I have either determined or contributed to structure determination, and structure/function and mechanistic elucidation in of a number of CAZY in [[GH5]], [[GH9]], [[GH10]], [[GH13]], [[GH26]], [[GH31]], [[GH36]], [[GH53]],[[PL4]] and [[AA9]]. Some of my articles on CAZYs are in the reference list below <cite>Harris1994</cite>, <cite>LeNours2004</cite>,<cite>Ernst2006</cite>,<cite>Ryttersgaard2002</cite>, <cite>LeNours2003</cite>, <cite>Ryttersgaard2004</cite>,<cite>LeNours2009</cite>.<br />
<br />
References<br />
---------<br />
<biblio><br />
#Jenkins1995 pmid=7729513<br />
#Henrissat1995 pmid=8643635 <br />
#Harris1994 pmid=7881909<br />
#LeNours2004 pmid=16171384<br />
#Ernst2006 pmid=16580018<br />
#Ryttersgaard2002 pmid=12484750 <br />
#LeNours2003 pmid=12761390<br />
#Ryttersgaard2004 pmid=15312766<br />
#LeNours2009 pmid=19089956 <br />
<br />
</biblio> <br />
<br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10301User:Leila LoLeggio2014-09-19T06:57:42Z<p>Leila LoLeggio: </p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily <cite>Jenkins1995</cite>, then to become Clan GH-A<cite>Henrissat1995</cite>.<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
<br />
I have either determined or contributed to structure determination, and structure/function and mechanistic elucidation in of a number of CAZY in [[GH5]], [[GH9]], [[GH10]], [[GH13]], [[GH26]], [[GH31]], [[GH36]], [[GH53]],[[PL4]] and [[AA9]]. Some of my articles on CAZYs are in the reference list below <cite>Harris1994</cite>, <cite>LeNours2004</cite>,<cite>Ernst2006</cite>,<cite>Ryttersgaard2002</cite> <cite>LeNours2003</cite><br />
<br />
References<br />
---------<br />
<biblio><br />
#Jenkins1995 pmid=7729513<br />
#Henrissat1995 pmid=8643635 <br />
#Harris1994 pmid=7881909<br />
#LeNours2004 pmid=16171384<br />
#Ernst2006 pmid=16580018<br />
#Ryttersgaard2002 pmid=2484750 <br />
#LeNours2003 pmid=12761390<br />
</biblio> <br />
<br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Sine_Larsen&diff=10300User:Sine Larsen2014-09-19T06:50:01Z<p>Leila LoLeggio: </p>
<hr />
<div>[[Image:SineLarsenPreciousPeople.jpg|200px|right]]<br />
<br />
Educated at University of Copenhagen, Post doc. at Massachusetts Institute of Technology (1970-71)<br />
<br />
Positions at Danish Technical University and University of Copenhagen, full professor since 1995.<br />
<br />
Broad research background in structural chemistry and structural biology.<br />
<br />
Director of Centre for Crystallographic Studies, Center of excellence funded by the Danish National Research Foundation to promote structural biology 1993-2004.<br />
<br />
Engaged in IUCr since 1996, General Secretary and Treasurer 1996-2005, president 2008-2011.<br />
<br />
Director of Research for Life Sciences European Synchrotron Radiation facility 2003-2009, Director of the<br />
<br />
MAX IV Laboratory 2011-2012, Member of Scientific advisory committees for several facilities.<br />
<br />
Currently professor at the Department of Chemistry, University of Copenhagen.<br />
<br />
CAZY interests have been primarily on structure determination of rhamnogalacturonan degrading enzymes.<br />
<br />
<br />
----<br />
<br />
<biblio><br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Larsen,Sine]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10299User:Leila LoLeggio2014-09-19T05:51:24Z<p>Leila LoLeggio: </p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily <cite>Jenkins1995</cite>, then to become Clan GH-A<cite>Henrissat1995</cite>.<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
<br />
I have either determined or contributed to structure determination, and structure/function and mechanistic elucidation in of a number of CAZY in [[GH5]], [[GH9]], [[GH10]], [[GH13]], [[GH26]], [[GH31]], [[GH36]], [[GH53]],[[PL4]] and [[AA9]]. Some of my articles on CAZYs are in the reference list below <cite>Harris1994</cite>, <cite>LeNours2004</cite>.<br />
<br />
References<br />
---------<br />
<biblio><br />
#Jenkins1995 pmid=7729513<br />
#Henrissat1995 pmid=8643635 <br />
#Harris1994 pmid=7881909<br />
#LeNours2004 pmid=16171384<br />
</biblio> <br />
<br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10298User:Leila LoLeggio2014-09-19T05:46:58Z<p>Leila LoLeggio: </p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily <cite>Jenkins1995</cite>, then to become Clan GH-A<cite>Henrissat1995</cite>.<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
<br />
I have either determined or contributed to structure determination, and structure/function and mechanistic elucidation in of a number of CAZY in [[GH5]], [[GH9]], [[GH10]], [[GH13]], [[GH26]], [[GH31]], [[GH36]], [[GH53]] and [[PL4]]. Some of my articles are in the reference list below.<br />
<br />
References<br />
---------<br />
<biblio><br />
#Jenkins1995 pmid=7729513<br />
#Henrissat1995 pmid=8643635 <br />
#Harris1994 pmid=7881909<br />
</biblio> <br />
<br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10297User:Leila LoLeggio2014-09-19T05:44:27Z<p>Leila LoLeggio: /* Short biographical sketch */</p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily <cite>Jenkins1995</cite>, then to become Clan GH-A<cite>Henrissat1995</cite>.<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
<br />
I have either determined or contributed to structure determination, and structure/function and mechanistic elucidation in of a number of CAZY in [[GH5]], [[GH9]], [[GH10]], [[GH13]], [[GH26]], [[GH31]], [[GH36]], [[GH53]] and [[PL4]]. Some of my articles are in the reference list below.<br />
<br />
References<br />
---------<br />
<biblio><br />
#Jenkins1995 pmid=7729513<br />
#Henrissat1995 pmid=8643635 <br />
</biblio> <br />
<br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Sine_Larsen&diff=10296User:Sine Larsen2014-09-19T05:41:17Z<p>Leila LoLeggio: </p>
<hr />
<div>[[Image:SineLarsenPreciousPeople.jpg|200px|right]]<br />
<br />
Sine Larsen is professor at the Department of Chemistry, University of Copenhagen.<br />
<br />
<br />
----<br />
<br />
<biblio><br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Larsen,Sine]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=File:SineLarsenPreciousPeople.jpg&diff=10295File:SineLarsenPreciousPeople.jpg2014-09-19T05:39:41Z<p>Leila LoLeggio: </p>
<hr />
<div></div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Sine_Larsen&diff=10294User:Sine Larsen2014-09-19T05:38:35Z<p>Leila LoLeggio: </p>
<hr />
<div>[[Image:Blank_user-200px.png|200px|right]]<br />
<br />
Sine Larsen is professor at the Department of Chemistry, University of Copenhagen.<br />
<br />
<br />
----<br />
<br />
<biblio><br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Larsen,Sine]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Sine_Larsen&diff=10293User:Sine Larsen2014-09-19T05:38:14Z<p>Leila LoLeggio: </p>
<hr />
<div>[[Image:Blank_user-200px.png|200px|right]]<br />
'''This is an empty template to help you get started with composing your User page.'''<br />
Sine Larsen is professor at the Department of Chemistry, University of Copenhagen.<br />
<br />
<br />
----<br />
<br />
<biblio><br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Larsen,Sine]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10292User:Leila LoLeggio2014-09-18T16:37:42Z<p>Leila LoLeggio: /* Short biographical sketch */</p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily <cite>Jenkins1995</cite>, then to become Clan GH-A<cite>Henrissat1995</cite>.<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
<br />
I have either determined or contributed to structure determination of a number of CAZY in [[GH5]], [[GH9]], [[GH10]], [[GH13]], [[GH26]], [[GH31]], [[GH36]], [[GH53]] and [[PL4]].<br />
<br />
<biblio><br />
#Jenkins1995 pmid=7729513<br />
#Henrissat1995 pmid=8643635 <br />
</biblio> <br />
<br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10291User:Leila LoLeggio2014-09-18T16:36:09Z<p>Leila LoLeggio: /* Short biographical sketch */</p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily <cite>Jenkins1995</cite>, then to become Clan GH-A.<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
<br />
I have either determined or contributed to structure determination of a number of CAZY in [[GH5]], [[GH9]], [[GH10]], [[GH13]], [[GH26]], [[GH31]], [[GH36]], [[GH53]] and [[PL4]].<br />
<br />
<biblio><br />
#Jenkins1995 pmid=7729513<br />
</biblio> <br />
<br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10290User:Leila LoLeggio2014-09-18T16:31:35Z<p>Leila LoLeggio: </p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily, then to become Clan GH-A [Jenkins1995].<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
<br />
I have either determined or contributed to structure determination of a number of CAZY in [[GH5]], [[GH9]], [[GH10]], [[GH13]], [[GH26]], [[GH31]], [[GH36]], [[GH53]] and [[PL4]].<br />
<br />
PubMed ID:7729513 <br />
<br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10289User:Leila LoLeggio2014-09-18T16:27:54Z<p>Leila LoLeggio: /* Short biographical sketch */</p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily, then to become Clan GH-A.<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
<br />
I have either determined or contributed to structure determination of a number of CAZY in [[GH5]], [[GH9]], [[GH10]], [[GH13]], [[GH26]], [[GH31]], [[GH36]], [[GH53]] and [[PL4]].<br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10288User:Leila LoLeggio2014-09-18T16:27:16Z<p>Leila LoLeggio: </p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily, then to become Clan GH-A.<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
<br />
I have either determined or contributed to structure determination of a number of CAZY in [[GH5]], [[GH9]], [[GH10]], [[GH13]], [[GH26]], [[GH31]], [[GH36]], [[GH53]]. <br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=User:Leila_LoLeggio&diff=10287User:Leila LoLeggio2014-09-18T15:59:06Z<p>Leila LoLeggio: </p>
<hr />
<div>[[File:Id_leila3.jpg|200px|right]]<br />
'''Associate Professor and Research Group leader''' at the Department of Chemistry, University of Copenhagen.<br />
<br />
== Short biographical sketch ==<br />
<br />
Italian, born in Palermo 1971. Educated in Biochemistry at the University of Bath, during which had two inspiring introductions to the world of research in the groups of Roy Jones at the Babraham station and Angelika Noegel at the Max-Planck Institute for Biochemistry in Munich. Obtained a PhD in Crystallography from Birkbeck College, London, in 1997. In fact my PhD research was carried out at the Institute of Food Research in Reading, under the supervision of ^^^Richard Pickersgill^^^. The project revolved around structure determination of xylanases and cellulases, and I was fortunate by being involved in the establishment of the 4/7 superfamily, then to become Clan GH-A.<br />
<br />
I was then post-doctoral fellow in the group of ^^^Sine Larsen^^^, at the Department of Chemistry, University of Copenhagen, first funded by a personal EMBO fellowship and later by other grants, until 2003, when I obtained a permanent position as Associate Professor in the same Department. In 2005 I became Research Group leader of the Biophysical Chemistry Group, still in the same Department. In 2013 the Biophysical Chemistry Group became part of the Bioinorganic and Biophysical Chemistry Section. Studies on the structure and function of carbohydrate active enzymes remains one of my major areas of research here in Copenhagen. My other main branch of research is on transcription factors.<br />
[[Category:Contributors|LoLeggio, Leila]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=File:Id_leila3.jpg&diff=10286File:Id leila3.jpg2014-09-18T15:57:52Z<p>Leila LoLeggio: </p>
<hr />
<div></div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10155Polysaccharide Lyase Family 42014-09-07T08:52:53Z<p>Leila LoLeggio: /* Three-dimensional structures */</p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies of a ligand complex (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:Figure_complex_PL4.png|thumb|300px|right|'''Structure of AaRGL4 K150A in complex with a hexasaccharide.''' Domain I is in magenta, domain II in cyan, and domain III in blue. The product is shown in sphere representation. Figure made in [http://pymol.org pymol]]]<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite> [[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a complex of the K150A catalytically impaired variant with substrate bound from -3 to +3 subsites[[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure depositions can be found searching with the given PDB code at the [[http://www.rcsb.org/ Protein Data Bank]].<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10154Polysaccharide Lyase Family 42014-09-07T08:52:03Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies of a ligand complex (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:Figure_complex_PL4.png|thumb|300px|right|'''Structure of an AaRGL4 in complex with a digestion product.''' Domain I is in magenta, domain II in cyan, and domain III in blue. The product is shown in sphere representation. Figure made in [http://pymol.org pymol]]]<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite> [[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a complex of the K150A catalytically impaired variant with substrate bound from -3 to +3 subsites[[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure depositions can be found searching with the given PDB code at the [[http://www.rcsb.org/ Protein Data Bank]].<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10153Polysaccharide Lyase Family 42014-09-07T08:49:59Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies of a ligand complex (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:Figure_complex_PL4.png|thumb|300px|right|'''Structure of an AaRGL4 in complex with a digestion product.''' Domain I is in magenta, domain II in cyan, and domain III in blue. The product is shown in sphere representation. Figure made in [http://pymol.org pymol]]].<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>[[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a complex of the K150A catalytically impaired variant with substrate bound from -3 to +3 subsites[[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure depositions can be found searching with the given PDB code at the [[http://www.rcsb.org/ Protein Data Bank]].<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10152Polysaccharide Lyase Family 42014-09-07T08:48:30Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies of a ligand complex (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:Figure_complex_PL4.png|thumb|300px|right|'''''''''Structure of an AaRGL4 in complex with a digestion product''' Domain I is in magenta, domain II in cyan, and domain III in blue. The product is shown in sphere representation. Figure made in [[http://pymol.org pymol]]]].<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>[[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a complex of the K150A catalytically impaired variant with substrate bound from -3 to +3 subsites[[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure depositions can be found searching with the given PDB code at the [[http://www.rcsb.org/ Protein Data Bank]].<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10151Polysaccharide Lyase Family 42014-09-07T08:47:09Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies of a ligand complex (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:Figure_complex_PL4.png|thumb|300px|right|'''''''''Structure of an AaRGL4 in complex with a digestion product''' Domain I is in magenta, domain II in cyan, and domain III in blue. The product is shown in sphere representation. Figure made in [[http://pymol.org pymol]]].<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>[[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a complex of the K150A catalytically impaired variant with substrate bound from -3 to +3 subsites[[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure depositions can be found searching with the given PDB code at the [[http://www.rcsb.org/ Protein Data Bank]].<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10150Polysaccharide Lyase Family 42014-09-07T08:45:51Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies of a ligand complex (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:Figure_complex_PL4.png|thumb|300px|right|'''''''''Structure of an AaRGL4 in complex with a digestion product''' Domain I is in magenta, domain II in cyan, and domain III in blue. The product is shown in sphere representation. Figure made in [[http://pymol.org pymol]].<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>[[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a complex of the K150A catalytically impaired variant with substrate bound from -3 to +3 subsites[[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure depositions can be found searching with the given PDB code at the [[http://www.rcsb.org/ Protein Data Bank]].<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10149Polysaccharide Lyase Family 42014-09-07T08:41:42Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[File:product_complex_PL4.png|thumb|300px|right|'''''''''Structure of an AaRGL4 in complex with a digestion product''' Domain I is in magenta, domain II in cyan, and domain III in blue. The product is shown in sphere representation. Figure made in [http://pymol.org pymol]]<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>[[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a product complex [[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure depositions can be found searching with the given PDB code at the [[http://www.rcsb.org/ Protein Data Bank]].<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=File:Figure_complex_PL4.png&diff=10148File:Figure complex PL4.png2014-09-07T08:36:35Z<p>Leila LoLeggio: </p>
<hr />
<div></div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10147Polysaccharide Lyase Family 42014-09-07T08:20:52Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>[[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a product complex [[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure depositions can be found searching with the given PDB code at the [[http://www.rcsb.org/ Protein Data Bank]].<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10146Polysaccharide Lyase Family 42014-09-07T08:20:08Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>[[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a product complex [[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure deposition can be found searching with the given PDB code at the [[http://www.rcsb.org/ Protein Data Bank]].<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10145Polysaccharide Lyase Family 42014-09-07T08:18:35Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>[[{{PDBlink}}1nkg 1NKG]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a product complex [[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>. Note that structure links in this page are to protopedia, while original structure deposition can be found searching with the given PDB code at the [http:/www.rcsb.org/ Protein Data Bank].<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10144Polysaccharide Lyase Family 42014-09-07T08:08:56Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>[[{{PDBlink}}1nkg 1NKg]], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [[{{PDBlink}}2xhn 2XHN], [{{PDBlink}}3njx 3NJX]]and a product complex [[{{PDBlink}}3njv 3NJV]]have been also determined <cite>Jensen2010</cite>.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10143Polysaccharide Lyase Family 42014-09-07T08:07:02Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>[{{PDBlink}}1ngk 1NGK], revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants [{{PDBlink}}2xhn 2XHN, {{PDBlink}}3njx 3NJX]and a product complex [{{PDBlink}}3njv 3NJV]have been also determined <cite>Jensen2010</cite>.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10142Polysaccharide Lyase Family 42014-09-07T08:00:47Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three-dimensional structure of PL4 rhamnogalacturonan lyase from ''Aspergillus aculeatus'' AaRGL4 <cite>McDonough2004</cite>, revealed that it is shaped as a flattened oval disk of approximate dimensions 90 x 58 x 40&Aring;. The secondary structure is predominantly &beta;-sheet arranged into three distinct modular domains, I, II and III. The N-terminal domain I, containing the catalytic residues and formed by residues 1-257, is folded into a β-super-sandwich, the fold of domain II comprised by residues 258-336 has a topology that is similar to fibronectin type III (FnIII). The residues 337-508 form the C-terminal domain III which displays a jelly roll β-sandwich fold and is structurally homologous to carbohydrate binding modules. The C-terminal hosts a structural calcium ion, not thought to be involved in catalysis. The structures of catalytic residues variants and a product complex have been also determined <cite>Jensen2010</cite>.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10141Polysaccharide Lyase Family 42014-09-07T07:49:49Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10140Polysaccharide Lyase Family 42014-09-07T07:48:59Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In [http://www.cazy.org/ CAZy database]<cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10139Polysaccharide Lyase Family 42014-09-07T07:46:16Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to [[PL1]], have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10138Polysaccharide Lyase Family 42014-09-07T07:42:14Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases such as pectate lyases, which tend to have rather basic pH optima. Another major difference to the pectate and other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite>Mayans1997</cite>, which despite belonging to PL1, have diverged significantly from the other members of the family which are pectate lyases. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Mayans1997 pmid=9195887<br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10137Polysaccharide Lyase Family 42014-09-07T07:34:32Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from subfamily 2, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases, which tend to have rather basic pH optima. Another major difference to other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite></cite>. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10136Polysaccharide Lyase Family 42014-09-07T07:30:23Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-{{smallcaps|d}}-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- {{smallcaps|d}}-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases, which tend to have rather basic pH optima. Another major difference to other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite></cite>. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10131Polysaccharide Lyase Family 42014-09-05T07:41:05Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- D-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases, which tend to have rather basic pH optima. Another major difference to other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite></cite>. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First proton abstractor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First proton donor identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10130Polysaccharide Lyase Family 42014-09-05T07:39:04Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- D-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases, which tend to have rather basic pH optima. Another major difference to other polysaccharide lyase mechanisms, is that divalent metal ions are not required by PL4 for catalysis. Both the low pH optimum and the lack of strict metal requirement show parallels between the PL4 mechanism and the mechanism of pectin lyases <cite></cite>. A mechanism for PL4 has been proposed based on mutagenesis and structural studies in complex with a reaction product (see below)<cite>Jensen2010</cite>.<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure <cite>McDonough2004</cite>, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210<cite>Jensen2010</cite>. In the proposed mechanism <cite>Jensen2010</cite>, based both on mutagenesis and structural considerations, Lys150 is the proton abstractor, while His210 plays the role of proton donor. In most other polysaccharide lyase mechanisms a proton donor has not been identified. A Lys as proton abstractor seems in conflict with the low pH optimum, but pKa calculations with a model of a substrate complex suggest that desolvation effects may help lower the pKa of this residue <cite>Jensen2010</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First catalytic base identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First general acid/base residue identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>McDonough2004</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#McDonough2004 pmid=15135077<br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10129Polysaccharide Lyase Family 42014-09-05T07:21:40Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- D-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound <cite>Jensen2010</cite>. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. The branching effects may account for the fact that some experiments have shown an average size of 25-30 sugar units in complete digestions of rhamnogalacturonan I by AaRGL4 <cite>Jensen2010</cite>.In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond in the non-reducing D-gactopyranosyluronic acid unit. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism. <br />
<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis in AaRGL4 to be Lys150 and His210. <br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First catalytic base identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First general acid/base residue identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Jensen2010</cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite></cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Jensen2010 pmid=20851126<br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10128Polysaccharide Lyase Family 42014-09-05T06:31:44Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Leila LoLeggio^^^ and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) <cite>Kofod1994</cite> cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- D-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism. <br />
<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First catalytic base identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite></cite>.<br />
;First general acid/base residue identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite></cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite></cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Kofod1994 pmid=7961884<br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10127Polysaccharide Lyase Family 42014-09-05T06:23:49Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: Leila Lo Leggio and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- D-galacturonic acid at the non-reducing end <cite>Azadi1995</cite>. Other biochemical studies <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism. <br />
<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First catalytic base identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite></cite>.<br />
;First general acid/base residue identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite></cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite></cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10126Polysaccharide Lyase Family 42014-09-05T06:09:13Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: Leila Lo Leggio and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product <cite>Azadi1995</cite> with &alpha;-&Delta;-(4,5)- D-galacturonic acid at the non-reducing end <cite>Mutter1998</cite>. the same study <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism. <br />
<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite>Azadi1995</cite>.<br />
;First catalytic base identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite></cite>.<br />
;First general acid/base residue identification: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite></cite>.<br />
;First 3-D structure: ''Aspergillus aculeatus'' Rhamnogalacturonan lyase <cite></cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Azadi1995 pmid=8720076<br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10125Polysaccharide Lyase Family 42014-09-05T06:01:18Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: Leila Lo Leggio and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&Delta;-(4,5)- D-galacturonic acid at the non-reducing end <cite>Mutter1998</cite>. the same study <cite>Mutter1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound. The effect of branching depends on the nature of the side chains, as removal of arabinan chains increases activity, while removal of galactose side chains reduces activity <cite>Mutter1998</cite>. In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4 <cite>Mutter1998</cite>) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism. <br />
<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: Content is to be added here.<br />
;First catalytic base identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: Content is to be added here.<br />
<br />
== References ==<br />
<biblio><br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10124Polysaccharide Lyase Family 42014-09-05T05:52:01Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: Leila Lo Leggio and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;--(4,5)- D-galacturonic acid at the non-reducing end. Biochemical studies <cite>Mutter 1998</cite> showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound. The effect of longer branching is not clear cut, as Mutter et al reported that removal of arabinan chains increases activity, while removal of galactose side chains reduces activity. In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism. <br />
<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: Content is to be added here.<br />
;First catalytic base identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: Content is to be added here.<br />
<br />
== References ==<br />
<biblio><br />
#Mutter1998 pmid=9576783<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10123Polysaccharide Lyase Family 42014-09-05T05:46:51Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: Leila Lo Leggio and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. Both rhamnose and galacturonic acid units are present in Rhamnogalacturonan I in their pyranose forms. Characterized PL4 enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzyme in the family, the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4) cleaves the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids, and produces an unsaturated product with &alpha;-&DELTA;-(4,5)- D-galacturonic acid at the non-reducing end. Biochemical studies [#Mutter1998 pmid=9576783] showed that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound. The effect of longer branching is not clear cut, as Mutter et al reported that removal of arabinan chains increases activity, while removal of galactose side chains reduces activity. In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism. <br />
<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: Content is to be added here.<br />
;First catalytic base identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: Content is to be added here.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10122Polysaccharide Lyase Family 42014-09-05T05:34:57Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: Leila Lo Leggio and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. These enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.23 4.2.2.23]) The best characterized enzymes in the family, exemplified by the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4)cleave the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids. Biochemical studies by Mutter et al. show that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound. The effect of longer branching is not clear cut, as Mutter et al reported that removal of arabinan chains increases activity, while removal of galactan side chains reduces activity. In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism. <br />
<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: Content is to be added here.<br />
;First catalytic base identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: Content is to be added here.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggiohttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_4&diff=10121Polysaccharide Lyase Family 42014-09-05T05:31:33Z<p>Leila LoLeggio: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: Leila Lo Leggio and Sine Larsen<br />
* [[Responsible Curator]]: ^^^Leila LoLeggio^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL4'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Charge neutraliser'''<br />
|none<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL4.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
<br />
The main activity assigned to characterized enzymes in PL4 is degradation of the plant cell wall component rhamnogalacturonan I, a component of pectin hairy regions. Rhamnogalacturonan I is a heteropolymer built up by the disaccharide unit [&alpha;-L-Rha-(1,4)-&alpha;-D-GalUA-(1,2)], with often extensive branching (arabinans, galactans and arabinogalactans)at the O2 and O3 of the galacturonic acid units. These enzymes are therefore Rhamnogalacturonan lyases (EC [{{EClink}}4.2.2.- 4.2.2.-]) The best characterized enzymes in the family, exemplified by the ''Aspergillus aculeatus'' Rhamnogalacturonan Lyase (AaRGL4)cleave the &alpha;-1,4-glycosidic bonds between L-rhamnose and D-galacturonic acids. Biochemical studies by Mutter et al. show that the minimum substrate requirement is a deacetylated dodecamer, with preferential cleavage four residues from the reducing end Rha, but the structural studies (see below) have demonstrated that smaller ligands can be bound. The effect of longer branching is not clear cut, as Mutter et al reported that removal of arabinan chains increases activity, while removal of galactan side chains reduces activity. In CAZY <cite>DaviesSinnott2008 Cantarel2009</cite>, PL4 is divided in 5 subfamilies with members from bacterial and eukaryotic kingdoms (fungi and plants). Apart from one of the subfamilies, consisting primarily of plant members, the subfamilies do not seem to follow phylogenetic divisions, and may reflect yet undiscovered differences in substrate preferences. <br />
<br />
== Kinetics and Mechanism ==<br />
Degradation of rhamnogalacturonan is via &beta;-elimination, which introduces a double bond. The optimum pH of activity is low (pH 6.00 as reported for AaRGL4) compared to other polysaccharide lyases, which tend to have rather basic pH optima. This has profound implications for the mechanism. <br />
<br />
== Catalytic Residues ==<br />
Catalytic residues were first suggested on the basis of sequence conservation and location on the 3D structure, and subsequently verified by site directed mutagenesis.<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
== Family Firsts ==<br />
;First demonstration of unsaturated product: Content is to be added here.<br />
;First catalytic base identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: Content is to be added here.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL004]]</div>Leila LoLeggio