3vpl

From Proteopedia

(Difference between revisions)

Revision as of 21:03, 5 August 2016

Crystal structure of a 2-fluoroxylotriosyl complex of the Vibrio sp. AX-4 Beta-1,3-xylanase

Structural highlights

3vpl is a 1 chain structure with sequence from Vibsx. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	xyl4 (VIBSX)
Activity:	Endo-1,3-beta-xylanase, with EC number 3.2.1.32
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[3XYN1_VIBSX] Catalyzes the hydrolysis of beta-1,3-xylan into oligosaccharides, mainly xylobiose, xylotriose and xylotetraose. Converts beta-1,3-xylotriose into xylose and xylobiose, converts beta-1,3-xylotetraose mainly into xylotriose and xylose, converts beta-1,3-xylopentaose into xylobiose and xylotriose. Does not hydrolyze beta-1,4-xylan, beta-1,4-mannan, beta-1,4-glucan, beta-1,3-xylobiose or p-nitrophenyl-beta-xyloside.^[1]

Publication Abstract from PubMed

Xylanases capable of degrading the crystalline microfibrils of 1,3-xylan that reinforce the cell walls of some red and siphonous green algae have not been well studied, yet they could prove to be of great utility in algaculture for the production of food and renewable chemical feedstocks. To gain a better mechanistic understanding of these enzymes, a suite of reagents was synthesized and evaluated as substrates and inhibitors of an endo-1,3-xylanase. With these reagents, a retaining mechanism was confirmed for the xylanase, its catalytic nucleophile identified, and the existence of -3 to +2 substrate-binding subsites demonstrated. Protein crystal X-ray diffraction methods provided a high resolution structure of a trapped covalent glycosyl-enzyme intermediate, indicating that the 1,3-xylanases likely utilize the (1)S(3) --> (4)H(3) --> (4)C(1) conformational itinerary to effect catalysis.

Mechanistic insights into the 1,3-xylanases: useful enzymes for manipulation of algal biomass.,Goddard-Borger ED, Sakaguchi K, Reitinger S, Watanabe N, Ito M, Withers SG J Am Chem Soc. 2012 Feb 29;134(8):3895-902. doi: 10.1021/ja211836t. Epub 2012 Feb, 16. PMID:22296113^[2]

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

References

↑ Kiyohara M, Sakaguchi K, Yamaguchi K, Araki T, Nakamura T, Ito M. Molecular cloning and characterization of a novel beta-1,3-xylanase possessing two putative carbohydrate-binding modules from a marine bacterium Vibrio sp. strain AX-4. Biochem J. 2005 Jun 15;388(Pt 3):949-57. PMID:15743273 doi:http://dx.doi.org/10.1042/BJ20050190
↑ Goddard-Borger ED, Sakaguchi K, Reitinger S, Watanabe N, Ito M, Withers SG. Mechanistic insights into the 1,3-xylanases: useful enzymes for manipulation of algal biomass. J Am Chem Soc. 2012 Feb 29;134(8):3895-902. doi: 10.1021/ja211836t. Epub 2012 Feb, 16. PMID:22296113 doi:http://dx.doi.org/10.1021/ja211836t

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/3vpl"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a 2-fluoroxylotriosyl complex of the Vibrio sp. AX-4 Beta-1,3-xylanase==
 <StructureSection load='3vpl' size='340' side='right' caption='[[3vpl]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3vpl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibrio_sp. Vibrio sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VPL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3vpl]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibsx Vibsx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VPL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VPL FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DNX:3,4-DINITROPHENOL'>DNX</scene>, <scene name='pdbligand=BXF:2-DEOXY-2-FLUORO-BETA-D-XYLOPYRANOSE'>BXF</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xyl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=678 Vibrio sp.])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xyl4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=678 VIBSX])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,3-beta-xylanase Endo-1,3-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.32 3.2.1.32] </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=3vpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vpl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vpl RCSB], [http://www.ebi.ac.uk/pdbsum/3vpl PDBsum]</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=3vpl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vpl OCA], [http://pdbe.org/3vpl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vpl RCSB], [http://www.ebi.ac.uk/pdbsum/3vpl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vpl ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3vpl" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 23: / Line 25: @@
 </StructureSection>
 [[Category: Endo-1,3-beta-xylanase]]
-[[Category: Vibrio sp]]
+[[Category: Vibsx]]
 [[Category: Sakaguchi, K]]
 [[Category: Watanabe, N]]

3vpl

From Proteopedia

Revision as of 21:03, 5 August 2016

Crystal structure of a 2-fluoroxylotriosyl complex of the Vibrio sp. AX-4 Beta-1,3-xylanase

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox