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2zbl

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Revision as of 19:55, 5 August 2016

Functional annotation of Salmonella enterica yihS-encoded protein

Structural highlights

2zbl is a 6 chain structure. 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

[SQUS_SALTY] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF) (By similarity). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, but has extremely low activity with glucose.[HAMAP-Rule:MF_00998]^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The three-dimensional structure of a Salmonella enterica hypothetical protein YihS is significantly similar to that of N-acyl-D-glucosamine 2-epimerase (AGE) with respect to a common scaffold, an alpha6/alpha6-barrel, although the function of YihS remains to be clarified. To identify the function of YihS, Escherichia coli and S. enterica YihS proteins were overexpressed in E. coli, purified, and characterized. Both proteins were found to show no AGE activity but showed cofactor-independent aldose-ketose isomerase activity involved in the interconversion of monosaccharides, mannose, fructose, and glucose, or lyxose and xylulose. In order to clarify the structure/function relationship of YihS, we determined the crystal structure of S. enterica YihS mutant (H248A) in complex with a substrate (D-mannose) at 1.6 A resolution. This enzyme-substrate complex structure is the first demonstration in the AGE structural family, and it enables us to identify active-site residues and postulate a reaction mechanism for YihS. The substrate, beta-d-mannose, fits well in the active site and is specifically recognized by the enzyme. The substrate-binding site of YihS for the mannose C1 and O5 atoms is architecturally similar to those of mutarotases, suggesting that YihS adopts the pyranose ring-opening process by His383 and acidifies the C2 position, forming an aldehyde at the C1 position. In the isomerization step, His248 functions as a base catalyst responsible for transferring the proton from the C2 to C1 positions through a cis-enediol intermediate. On the other hand, in AGE, His248 is thought to abstract and re-adduct the proton at the C2 position of the substrate. These findings provide not only molecular insights into the YihS reaction mechanism but also useful information for the molecular design of novel carbohydrate-active enzymes with the common scaffold, alpha6/alpha6-barrel.

Crystal structure of YihS in complex with D-mannose: structural annotation of Escherichia coli and Salmonella enterica yihS-encoded proteins to an aldose-ketose isomerase.,Itoh T, Mikami B, Hashimoto W, Murata K J Mol Biol. 2008 Apr 11;377(5):1443-59. Epub 2008 Feb 12. PMID:18328504^[2]

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

References

↑ Itoh T, Mikami B, Hashimoto W, Murata K. Crystal structure of YihS in complex with D-mannose: structural annotation of Escherichia coli and Salmonella enterica yihS-encoded proteins to an aldose-ketose isomerase. J Mol Biol. 2008 Apr 11;377(5):1443-59. Epub 2008 Feb 12. PMID:18328504 doi:10.1016/j.jmb.2008.01.090
↑ Itoh T, Mikami B, Hashimoto W, Murata K. Crystal structure of YihS in complex with D-mannose: structural annotation of Escherichia coli and Salmonella enterica yihS-encoded proteins to an aldose-ketose isomerase. J Mol Biol. 2008 Apr 11;377(5):1443-59. Epub 2008 Feb 12. PMID:18328504 doi:10.1016/j.jmb.2008.01.090

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2zbl"

@@ Line 1: / Line 1: @@
 ==Functional annotation of Salmonella enterica yihS-encoded protein==
 <StructureSection load='2zbl' size='340' side='right' caption='[[2zbl]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zbl]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZBL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zbl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZBL FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yihS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</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=2zbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zbl OCA], [http://pdbe.org/2zbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zbl RCSB], [http://www.ebi.ac.uk/pdbsum/2zbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zbl ProSAT]</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=2zbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zbl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zbl RCSB], [http://www.ebi.ac.uk/pdbsum/2zbl PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q8ZKT7_SALTY Q8ZKT7_SALTY]] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF) (By similarity). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, but has extremely low activity with glucose.<ref>PMID:18328504</ref>
+[[http://www.uniprot.org/uniprot/SQUS_SALTY SQUS_SALTY]] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF) (By similarity). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, but has extremely low activity with glucose.[HAMAP-Rule:MF_00998]<ref>PMID:18328504</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 17: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zbl ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2zbl" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
 [[Category: Hashimoto, W]]
 [[Category: Itoh, T]]

2zbl

From Proteopedia

Revision as of 19:55, 5 August 2016

Functional annotation of Salmonella enterica yihS-encoded protein

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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