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1gny

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Revision as of 08:00, 11 January 2023

xylan-binding module CBM15

Structural highlights

1gny is a 1 chain structure with sequence from Cellvibrio japonicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

XY10C_CELJA Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.^[1] ^[2]

Publication Abstract from PubMed

The recycling of photosynthetically fixed carbon by the action of microbial glycoside hydrolases is a key biological process. The consortium of degradative enzymes involved in this process frequently display catalytic modules appended to one or more noncatalytic carbohydrate-binding modules (CBMs). CBMs play a central role in the optimization of the catalytic activity of plant cell wall hydrolases through their binding to specific plant structural polysaccharides. Despite their pivotal role in the biodegradation of plant biomass, the mechanism by which these proteins recognize their target ligands is unclear. This report describes the structure of a xylan-binding CBM (CBM15) in complex with its ligand. This module, derived from Pseudomonas cellulosa xylanase Xyn10C, binds to both soluble xylan and xylooligosaccharides. The three-dimensional crystal structure of CBM15 bound to xylopentaose has been solved by x-ray crystallography to a resolution of 1.6 A. The protein displays a similar beta-jelly roll fold to that observed in many other families of binding-modules. A groove, 20-25 A in length, on the concave surface of one of the beta-sheets presents two tryptophan residues, the faces of which are orientated at approximately 240 degrees to one another. These form-stacking interactions with the n and n+2 sugars of xylopentaose complementing the approximate 3-fold helical structure of this ligand in the binding cleft of CBM15. In four of the five observed binding subsites, the 2' and 3' hydroxyls of the bound ligand are solvent-exposed, providing an explanation for the capacity of this xylan-binding CBM to accommodate the highly decorated xylans found in the plant cell wall.

Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation.,Szabo L, Jamal S, Xie H, Charnock SJ, Bolam DN, Gilbert HJ, Davies GJ J Biol Chem. 2001 Dec 28;276(52):49061-5. Epub 2001 Oct 11. PMID:11598143^[3]

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

References

↑ Pell G, Szabo L, Charnock SJ, Xie H, Gloster TM, Davies GJ, Gilbert HJ. Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases. J Biol Chem. 2004 Mar 19;279(12):11777-88. Epub 2003 Dec 11. PMID:14670951 doi:10.1074/jbc.M311947200
↑ Millward-Sadler SJ, Davidson K, Hazlewood GP, Black GW, Gilbert HJ, Clarke JH. Novel cellulose-binding domains, NodB homologues and conserved modular architecture in xylanases from the aerobic soil bacteria Pseudomonas fluorescens subsp. cellulosa and Cellvibrio mixtus. Biochem J. 1995 Nov 15;312 ( Pt 1):39-48. PMID:7492333
↑ Szabo L, Jamal S, Xie H, Charnock SJ, Bolam DN, Gilbert HJ, Davies GJ. Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation. J Biol Chem. 2001 Dec 28;276(52):49061-5. Epub 2001 Oct 11. PMID:11598143 doi:http://dx.doi.org/10.1074/jbc.M109558200

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1gny"

@@ Line 3: / Line 3: @@
 <StructureSection load='1gny' size='340' side='right'caption='[[1gny]], [[Resolution|resolution]] 1.63&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"cellvibrio_cellulosa"_nagy_et_al._2002 "cellvibrio cellulosa" nagy et al. 2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GNY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GNY FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [https://pdbe.org/1gny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [https://www.ebi.ac.uk/pdbsum/1gny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gny ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/XY10C_CELJA XY10C_CELJA]] Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.<ref>PMID:14670951</ref> <ref>PMID:7492333</ref>
+[https://www.uniprot.org/uniprot/XY10C_CELJA XY10C_CELJA] Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.<ref>PMID:14670951</ref> <ref>PMID:7492333</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Cellvibrio cellulosa nagy et al. 2002]]
+[[Category: Cellvibrio japonicus]]
-[[Category: Endo-1,4-beta-xylanase]]
 [[Category: Large Structures]]
-[[Category: Bolam, D N]]
+[[Category: Bolam DN]]
-[[Category: Charnock, S J]]
+[[Category: Charnock SJ]]
-[[Category: Davies, G J]]
+[[Category: Davies GJ]]
-[[Category: Gilbert, H J]]
+[[Category: Gilbert HJ]]
-[[Category: Jamal, S]]
+[[Category: Jamal S]]
-[[Category: Szabo, S]]
+[[Category: Szabo S]]
-[[Category: Xie, H]]
+[[Category: Xie H]]
-[[Category: Carbohydrate-binding module]]
-[[Category: Catalysis]]
-[[Category: Xylan]]
-[[Category: Xylanase]]
-[[Category: Xylooligosaccharide]]

1gny

From Proteopedia

Revision as of 08:00, 11 January 2023

xylan-binding module CBM15

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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