2f2h: Difference between revisions

Revision as of 10:37, 17 February 2021

Structure of the YicI thiosugar Michaelis complex

Structural highlights

2f2h is a 6 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	GOL, MPO, SO4, XTG
Gene:	yicI ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[XYLS_ECOLI] Can catalyze the transfer of alpha-xylosyl residue from alpha-xyloside to xylose, glucose, mannose, fructose, maltose, isomaltose, nigerose, kojibiose, sucrose and trehalose.^[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

For the first time, the thioglycoligase strategy has been successfully applied to alpha-glycosidases. The alpha-thioglycoligases derived from the family 31 glycosidases, alpha-xylosidase from E. coli (YicI) and alpha-glucosidase from Sulfolobus solfataricus, catalyze thioglycoligase reactions using alpha-glycosyl fluorides and deoxythioglycosides as donors and acceptors, respectively, in yields up to 86%. In addition, we describe the Michaelis complex of YicI using one of the thioglycosides as a nonhydrolyzable substrate analogue and discuss the structural insights this yields into the specificity and mechanism of family 31 alpha-glycosidases and the molecular basis of an associated genetic disease.

Expanding the thioglycoligase strategy to the synthesis of alpha-linked thioglycosides allows structural investigation of the parent enzyme/substrate complex.,Kim YW, Lovering AL, Chen H, Kantner T, McIntosh LP, Strynadka NC, Withers SG J Am Chem Soc. 2006 Feb 22;128(7):2202-3. PMID:16478160^[3]

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

References

↑ Okuyama M, Mori H, Chiba S, Kimura A. Overexpression and characterization of two unknown proteins, YicI and YihQ, originated from Escherichia coli. Protein Expr Purif. 2004 Sep;37(1):170-9. PMID:15294295 doi:https://dx.doi.org/10.1016/j.pep.2004.05.008
↑ Lovering AL, Lee SS, Kim YW, Withers SG, Strynadka NC. Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate. J Biol Chem. 2005 Jan 21;280(3):2105-15. Epub 2004 Oct 22. PMID:15501829 doi:10.1074/jbc.M410468200
↑ Kim YW, Lovering AL, Chen H, Kantner T, McIntosh LP, Strynadka NC, Withers SG. Expanding the thioglycoligase strategy to the synthesis of alpha-linked thioglycosides allows structural investigation of the parent enzyme/substrate complex. J Am Chem Soc. 2006 Feb 22;128(7):2202-3. PMID:16478160 doi:10.1021/ja057904a

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Okuyama M, Mori H, Chiba S, Kimura A. Overexpression and characterization of two unknown proteins, YicI and YihQ, originated from Escherichia coli. Protein Expr Purif. 2004 Sep;37(1):170-9. PMID:15294295 doi:https://dx.doi.org/10.1016/j.pep.2004.05.008

[2] Lovering AL, Lee SS, Kim YW, Withers SG, Strynadka NC. Mechanistic and structural analysis of a family 31 alpha-glycosidase and its glycosyl-enzyme intermediate. J Biol Chem. 2005 Jan 21;280(3):2105-15. Epub 2004 Oct 22. PMID:15501829 doi:10.1074/jbc.M410468200

[3] Kim YW, Lovering AL, Chen H, Kantner T, McIntosh LP, Strynadka NC, Withers SG. Expanding the thioglycoligase strategy to the synthesis of alpha-linked thioglycosides allows structural investigation of the parent enzyme/substrate complex. J Am Chem Soc. 2006 Feb 22;128(7):2202-3. PMID:16478160 doi:10.1021/ja057904a

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Structure of the YicI thiosugar Michaelis complex==
-<StructureSection load='2f2h' size='340' side='right' caption='[[2f2h]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='2f2h' size='340' side='right'caption='[[2f2h]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2f2h]] 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=2F2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F2H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2f2h]] is a 6 chain structure with sequence from [https://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=2F2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F2H FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XTG:4-NITROPHENYL+6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>XTG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XTG:4-NITROPHENYL+6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE'>XTG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yicI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yicI ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2f2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f2h OCA], [http://pdbe.org/2f2h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f2h RCSB], [http://www.ebi.ac.uk/pdbsum/2f2h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2f2h 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=2f2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f2h OCA], [https://pdbe.org/2f2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f2h RCSB], [https://www.ebi.ac.uk/pdbsum/2f2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f2h ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/XYLS_ECOLI XYLS_ECOLI]] Can catalyze the transfer of alpha-xylosyl residue from alpha-xyloside to xylose, glucose, mannose, fructose, maltose, isomaltose, nigerose, kojibiose, sucrose and trehalose.<ref>PMID:15294295</ref> <ref>PMID:15501829</ref>
+[[https://www.uniprot.org/uniprot/XYLS_ECOLI XYLS_ECOLI]] Can catalyze the transfer of alpha-xylosyl residue from alpha-xyloside to xylose, glucose, mannose, fructose, maltose, isomaltose, nigerose, kojibiose, sucrose and trehalose.<ref>PMID:15294295</ref> <ref>PMID:15501829</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Bacillus coli migula 1895]]
+[[Category: Large Structures]]
 [[Category: Kim, Y W]]
 [[Category: Lovering, A L]]

2f2h: Difference between revisions

Revision as of 10:37, 17 February 2021

Structure of the YicI thiosugar Michaelis complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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