5nok: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 5nok is ~~ON HOLD until Paper~~ Publication

==Polysaccharide Lyase BACCELL_00875==

== Structural highlights ==

<table><tr><td colspan='2'>[[5nok]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NOK FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>

<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5nok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nok OCA], [http://pdbe.org/5nok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nok RCSB], [http://www.ebi.ac.uk/pdbsum/5nok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nok ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represents a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis we screened the potential enzymatic functions of hypothetical proteins encoded by genes of Bacteroides thetaiotaomicron that were up-regulated by arabinogalactan proteins or AGPs. Although AGPs are ubiquitous in plants, there is a paucity of information on their detailed structure, the function of these glycans in planta, and the mechanisms by which they are depolymerized in microbial ecosystems. Here we have discovered a new polysaccharide lyase family that is specific for the l-rhamnose-alpha1,4-d-glucuronic acid linkage that caps the side chains of complex AGPs. The reaction product generated by the lyase, Delta4,5-unsaturated uronic acid, is removed from AGP by a glycoside hydrolase located in family GH105, producing the final product 4-deoxy-beta-l-threo-hex-4-enepyranosyl-uronic acid. The crystal structure of a member of the novel lyase family revealed a catalytic domain that displays an (alpha/alpha)6 barrel-fold. In the center of the barrel is a deep pocket, which, based on mutagenesis data and amino acid conservation, comprises the active site of the lyase. A tyrosine is the proposed catalytic base in the beta-elimination reaction. This study illustrates how highly complex glycans can be used as a scaffold to discover new enzyme families within microbial ecosystems where carbohydrate metabolism is a major evolutionary driver.

~~Authors: Cartmell, A~~., Munoz-Munoz, J., Terrapon, N., Basle, A., Henrissat, B., Gilbert, ~~H.J~~.

An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins.,Munoz-Munoz J, Cartmell A, Terrapon N, Basle A, Henrissat B, Gilbert HJ J Biol Chem. 2017 Aug 11;292(32):13271-13283. doi: 10.1074/jbc.M117.794578. Epub , 2017 Jun 21. PMID:28637865<ref>PMID:28637865</ref>

~~Description~~: ~~Polysaccharide Lyase BACCELL_00875~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased Structures~~]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Basle, A]]

[[Category: Cartmell, A]]

[[Category: Gilbert, H J]]

[[Category: Henrissat, B]]

[[Category: Munoz-Munoz, J]]

[[Category: Terrapon, N]]

[[Category: ~~Munoz-Munoz, J~~]]

[[Category: Arabinogalactan]]

[[Category: ~~Cartmell, A~~]]

[[Category: Glucuronic acid]]

[[Category: ~~Basle, A~~]]

[[Category: L-rhamnose]]

[[Category: ~~Gilbert, H.J~~]]

[[Category: Lyase]]

[[Category: Polysaccharide lyase]]

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5nok is ON HOLD  until Paper Publication
+==Polysaccharide Lyase BACCELL_00875==
+<StructureSection load='5nok' size='340' side='right' caption='[[5nok]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5nok]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NOK FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5nok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nok OCA], [http://pdbe.org/5nok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nok RCSB], [http://www.ebi.ac.uk/pdbsum/5nok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nok ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represents a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis we screened the potential enzymatic functions of hypothetical proteins encoded by genes of Bacteroides thetaiotaomicron that were up-regulated by arabinogalactan proteins or AGPs. Although AGPs are ubiquitous in plants, there is a paucity of information on their detailed structure, the function of these glycans in planta, and the mechanisms by which they are depolymerized in microbial ecosystems. Here we have discovered a new polysaccharide lyase family that is specific for the l-rhamnose-alpha1,4-d-glucuronic acid linkage that caps the side chains of complex AGPs. The reaction product generated by the lyase, Delta4,5-unsaturated uronic acid, is removed from AGP by a glycoside hydrolase located in family GH105, producing the final product 4-deoxy-beta-l-threo-hex-4-enepyranosyl-uronic acid. The crystal structure of a member of the novel lyase family revealed a catalytic domain that displays an (alpha/alpha)6 barrel-fold. In the center of the barrel is a deep pocket, which, based on mutagenesis data and amino acid conservation, comprises the active site of the lyase. A tyrosine is the proposed catalytic base in the beta-elimination reaction. This study illustrates how highly complex glycans can be used as a scaffold to discover new enzyme families within microbial ecosystems where carbohydrate metabolism is a major evolutionary driver.
-Authors: Cartmell, A., Munoz-Munoz, J., Terrapon, N., Basle, A., Henrissat, B., Gilbert, H.J.
+An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins.,Munoz-Munoz J, Cartmell A, Terrapon N, Basle A, Henrissat B, Gilbert HJ J Biol Chem. 2017 Aug 11;292(32):13271-13283. doi: 10.1074/jbc.M117.794578. Epub , 2017 Jun 21. PMID:28637865<ref>PMID:28637865</ref>
-Description: Polysaccharide Lyase BACCELL_00875
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5nok" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Basle, A]]
+[[Category: Cartmell, A]]
+[[Category: Gilbert, H J]]
 [[Category: Henrissat, B]]
+[[Category: Munoz-Munoz, J]]
 [[Category: Terrapon, N]]
-[[Category: Munoz-Munoz, J]]
+[[Category: Arabinogalactan]]
-[[Category: Cartmell, A]]
+[[Category: Glucuronic acid]]
-[[Category: Basle, A]]
+[[Category: L-rhamnose]]
-[[Category: Gilbert, H.J]]
+[[Category: Lyase]]
+[[Category: Polysaccharide lyase]]