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5a6m

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Revision as of 04:41, 25 May 2023

Determining the specificities of the catalytic site from the very high resolution structure of the thermostable glucuronoxylan endo-Beta-1, 4-xylanase, CtXyn30A, from Clostridium thermocellum with a xylotetraose bound

Structural highlights

5a6m is a 1 chain structure with sequence from Acetivibrio thermocellus ATCC 27405. 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

A3DJS9_ACET2

Publication Abstract from PubMed

Glucuronoxylan endo-beta-1,4-xylanases cleave the xylan chain specifically at sites containing 4-O-methylglucuronic acid substitutions. These enzymes have recently received considerable attention owing to their importance in the cooperative hydrolysis of heteropolysaccharides. However, little is known about the hydrolysis of glucuronoxylans in extreme environments. Here, the structure of a thermostable family 30 glucuronoxylan endo-beta-1,4-xylanase (CtXyn30A) from Clostridium thermocellum is reported. CtXyn30A is part of the cellulosome, a highly elaborate multi-enzyme complex secreted by the bacterium to efficiently deconstruct plant cell-wall carbohydrates. CtXyn30A preferably hydrolyses glucuronoxylans and displays maximum activity at pH 6.0 and 70 degrees C. The structure of CtXyn30A displays a (beta/alpha)8 TIM-barrel core with a side-associated beta-sheet domain. Structural analysis of the CtXyn30A mutant E225A, solved in the presence of xylotetraose, revealed xylotetraose-cleavage oligosaccharides partially occupying subsites -3 to +2. The sugar ring at the +1 subsite is held in place by hydrophobic stacking interactions between Tyr139 and Tyr200 and hydrogen bonds to the OH group of Tyr227. Although family 30 glycoside hydrolases are retaining enzymes, the xylopyranosyl ring at the -1 subsite of CtXyn30A-E225A appears in the alpha-anomeric configuration. A set of residues were found to be strictly conserved in glucuronoxylan endo-beta-1,4-xylanases and constitute the molecular determinants of the restricted specificity displayed by these enzymes. CtXyn30A is the first thermostable glucuronoxylan endo-beta-1,4-xylanase described to date. This work reveals that substrate recognition by both thermophilic and mesophilic glucuronoxylan endo-beta-1,4-xylanases is modulated by a conserved set of residues.

Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) from Clostridium thermocellum.,Freire F, Verma A, Bule P, Alves VD, Fontes CM, Goyal A, Najmudin S Acta Crystallogr D Struct Biol. 2016 Nov 1;72(Pt 11):1162-1173. Epub 2016 Oct 28. PMID:27841749^[1]

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

References

↑ Freire F, Verma A, Bule P, Alves VD, Fontes CM, Goyal A, Najmudin S. Conservation in the mechanism of glucuronoxylan hydrolysis revealed by the structure of glucuronoxylan xylanohydrolase (CtXyn30A) from Clostridium thermocellum. Acta Crystallogr D Struct Biol. 2016 Nov 1;72(Pt 11):1162-1173. Epub 2016 Oct 28. PMID:27841749 doi:http://dx.doi.org/10.1107/S2059798316014376

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/5a6m"

@@ Line 3: / Line 3: @@
 <StructureSection load='5a6m' size='340' side='right'caption='[[5a6m]], [[Resolution|resolution]] 1.17&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5a6m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A6M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5a6m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acetivibrio_thermocellus_ATCC_27405 Acetivibrio thermocellus ATCC 27405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A6M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A6M FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PRD_900116:4beta-beta-xylobiose'>PRD_900116</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5a6l|5a6l]]</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=5a6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a6m OCA], [https://pdbe.org/5a6m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a6m RCSB], [https://www.ebi.ac.uk/pdbsum/5a6m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a6m ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5a6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a6m OCA], [http://pdbe.org/5a6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5a6m RCSB], [http://www.ebi.ac.uk/pdbsum/5a6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5a6m ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A3DJS9_ACET2 A3DJS9_ACET2]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Endo-1,4-beta-xylanase]]
+[[Category: Acetivibrio thermocellus ATCC 27405]]
 [[Category: Large Structures]]
-[[Category: Bule, P]]
+[[Category: Bule P]]
-[[Category: Fontes, C M.G A]]
+[[Category: Fontes CMGA]]
-[[Category: Freire, F]]
+[[Category: Freire F]]
-[[Category: Goyal, A]]
+[[Category: Goyal A]]
-[[Category: Najmudin, S]]
+[[Category: Najmudin S]]
-[[Category: Verma, A K]]
+[[Category: Verma AK]]
-[[Category: Hydrolase]]

5a6m

From Proteopedia

Revision as of 04:41, 25 May 2023

Determining the specificities of the catalytic site from the very high resolution structure of the thermostable glucuronoxylan endo-Beta-1, 4-xylanase, CtXyn30A, from Clostridium thermocellum with a xylotetraose bound

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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