2f2h: Difference between revisions

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[[Image:2f2h.gif|left|200px]]


{{Structure
==Structure of the YicI thiosugar Michaelis complex==
|PDB= 2f2h |SIZE=350|CAPTION= <scene name='initialview01'>2f2h</scene>, resolution 1.950&Aring;
<StructureSection load='2f2h' size='340' side='right'caption='[[2f2h]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <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>
<table><tr><td colspan='2'>[[2f2h]] 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=2F2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F2H FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
|GENE= yicI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<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>
|DOMAIN=
<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>
|RELATEDENTRY=
</table>
|RESOURCES=<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://www.ebi.ac.uk/pdbsum/2f2h PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2f2h RCSB]</span>
== Function ==
}}
[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 ==
'''Structure of the YicI thiosugar Michaelis complex'''
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
 
  <jmolCheckbox>
==Overview==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f2/2f2h_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <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/main_output.php?pdb_ID=2f2h ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== 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.
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.


==About this Structure==
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<ref>PMID:16478160</ref>
2F2H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F2H OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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:[http://www.ncbi.nlm.nih.gov/pubmed/16478160 16478160]
</div>
<div class="pdbe-citations 2f2h" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Kim, Y W.]]
[[Category: Kim Y-W]]
[[Category: Lovering, A L.]]
[[Category: Lovering AL]]
[[Category: Strynadka, N C.J.]]
[[Category: Strynadka NCJ]]
[[Category: Withers, S G.]]
[[Category: Withers SG]]
[[Category: beta8alpha8 barrel]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:57:00 2008''

Latest revision as of 10:41, 23 August 2023

Structure of the YicI thiosugar Michaelis complexStructure of the YicI thiosugar Michaelis complex

Structural highlights

2f2h is a 6 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.95Å
Ligands:, , ,
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

  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:http://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

2f2h, resolution 1.95Å

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