5noa: Difference between revisions

Line 1:

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

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

==Polysaccharide Lyase BACCELL_00875==

== Structural highlights ==

<table><tr><td colspan='2'>[[5noa]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NOA FirstGlance]. <br>

</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Unsaturated_rhamnogalacturonyl_hydrolase Unsaturated rhamnogalacturonyl hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.172 3.2.1.172] </span></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=5noa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5noa OCA], [http://pdbe.org/5noa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5noa RCSB], [http://www.ebi.ac.uk/pdbsum/5noa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5noa 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: Unsaturated rhamnogalacturonyl hydrolase]]

[[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: Bacteroides thetaiotaomicron]]

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

[[Category: Gum arabic]]

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

[[Category: Human gut microbiota]]

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

[[Category: Hydrolase]]

[[Category: Polysaccharide lyase]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5noa is ON HOLD  until Paper Publication
+==Polysaccharide Lyase BACCELL_00875==
+<StructureSection load='5noa' size='340' side='right' caption='[[5noa]], [[Resolution|resolution]] 1.26&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5noa]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NOA FirstGlance]. <br>
+</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Unsaturated_rhamnogalacturonyl_hydrolase Unsaturated rhamnogalacturonyl hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.172 3.2.1.172] </span></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=5noa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5noa OCA], [http://pdbe.org/5noa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5noa RCSB], [http://www.ebi.ac.uk/pdbsum/5noa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5noa 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 5noa" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Unsaturated rhamnogalacturonyl hydrolase]]
+[[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: Bacteroides thetaiotaomicron]]
-[[Category: Cartmell, A]]
+[[Category: Gum arabic]]
-[[Category: Basle, A]]
+[[Category: Human gut microbiota]]
-[[Category: Gilbert, H.J]]
+[[Category: Hydrolase]]
+[[Category: Polysaccharide lyase]]