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| | ==Functional annotation of Escherichia coli yihS-encoded protein== | | ==Functional annotation of Escherichia coli yihS-encoded protein== |
| - | <StructureSection load='2rgk' size='340' side='right' caption='[[2rgk]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='2rgk' size='340' side='right'caption='[[2rgk]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2rgk]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RGK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2rgk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RGK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</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=562 "Bacillus coli" Migula 1895])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [http://pdbe.org/2rgk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [http://www.ebi.ac.uk/pdbsum/2rgk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rgk ProSAT]</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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [https://pdbe.org/2rgk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [https://www.ebi.ac.uk/pdbsum/2rgk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rgk ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SQUS_ECOLI SQUS_ECOLI]] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, or lyxose and xylulose, but has extremely low activity with glucose.[HAMAP-Rule:MF_00998]<ref>PMID:18328504</ref> <ref>PMID:24463506</ref> | + | [https://www.uniprot.org/uniprot/SQUS_ECOLI SQUS_ECOLI] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, or lyxose and xylulose, but has extremely low activity with glucose.[HAMAP-Rule:MF_00998]<ref>PMID:18328504</ref> <ref>PMID:24463506</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Hashimoto, W]] | + | [[Category: Large Structures]] |
| - | [[Category: Itoh, T]] | + | [[Category: Hashimoto W]] |
| - | [[Category: Mikami, B]] | + | [[Category: Itoh T]] |
| - | [[Category: Murata, K]] | + | [[Category: Mikami B]] |
| - | [[Category: Isomerase]]
| + | [[Category: Murata K]] |
| - | [[Category: N-acyl-d-glucosamine 2-epimerase protein family]]
| + | |
| Structural highlights
Function
SQUS_ECOLI Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, or lyxose and xylulose, but has extremely low activity with glucose.[HAMAP-Rule:MF_00998][1] [2]
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[3]
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
- ↑ Denger K, Weiss M, Felux AK, Schneider A, Mayer C, Spiteller D, Huhn T, Cook AM, Schleheck D. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle. Nature. 2014 Mar 6;507(7490):114-7. doi: 10.1038/nature12947. Epub 2014 Jan 26. PMID:24463506 doi:http://dx.doi.org/10.1038/nature12947
- ↑ 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
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