3mpb: Difference between revisions

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[[Image:3mpb.png|left|200px]]
==Z5688 from E. coli O157:H7 bound to fructose==
<StructureSection load='3mpb' size='340' side='right' caption='[[3mpb]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3mpb]] is a 2 chain structure with 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=3MPB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MPB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kmh|3kmh]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ECs5070, Z5688 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=3mpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mpb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3mpb RCSB], [http://www.ebi.ac.uk/pdbsum/3mpb PDBsum]</span></td></tr>
</table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mp/3mpb_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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Prokaryotes can use a variety of sugars as carbon sources in order to provide a selective survival advantage. The gene z5688 found in the pathogenic Escherichia coli O157:H7 encodes a "hypothetical" protein of unknown function. Sequence analysis identified the gene product as a putative member of the cupin superfamily of proteins, but no other functional information was known. We have determined the crystal structure of the Z5688 protein at 1.6 A resolution and identified the protein as a novel E. coli sugar isomerase (EcSI) through overall fold analysis and secondary-structure matching. Extensive substrate screening revealed that EcSI is capable of acting on d-lyxose and d-mannose. The complex structure of EcSI with fructose allowed the identification of key active-site residues, and mutagenesis confirmed their importance. The structure of EcSI also suggested a novel mechanism for substrate binding and product release in a cupin sugar isomerase. Supplementation of a nonpathogenic E. coli strain with EcSI enabled cell growth on the rare pentose d-lyxose.


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Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli O157:H7.,van Staalduinen LM, Park CS, Yeom SJ, Adams-Cioaba MA, Oh DK, Jia Z J Mol Biol. 2010 Sep 3;401(5):866-81. Epub 2010 Jul 6. PMID:20615418<ref>PMID:20615418</ref>
The line below this paragraph, containing "STRUCTURE_3mpb", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
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{{STRUCTURE_3mpb|  PDB=3mpb  |  SCENE=  }}


===Z5688 from E. coli O157:H7 bound to fructose===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
 
== References ==
<!--
<references/>
The line below this paragraph, {{ABSTRACT_PUBMED_20615418}}, adds the Publication Abstract to the page
__TOC__
(as it appears on PubMed at http://www.pubmed.gov), where 20615418 is the PubMed ID number.
</StructureSection>
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{{ABSTRACT_PUBMED_20615418}}
 
==About this Structure==
[[3mpb]] is a 2 chain structure with 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=3MPB OCA].
 
==Reference==
<ref group="xtra">PMID:20615418</ref><references group="xtra"/>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: BSGI, Montreal-Kingston Bacterial Structural Genomics Initiative.]]
[[Category: Structural genomic]]
[[Category: Jia, Z.]]
[[Category: Jia, Z]]
[[Category: Staalduinen, L M.van.]]
[[Category: Staalduinen, L M.van]]
[[Category: Beta barrel]]
[[Category: Bsgi]]
[[Category: Cupin]]
[[Category: Isomerase]]

Revision as of 19:10, 18 December 2014

Z5688 from E. coli O157:H7 bound to fructoseZ5688 from E. coli O157:H7 bound to fructose

Structural highlights

3mpb is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , ,
Gene:ECs5070, Z5688 (Escherichia coli)
Resources:FirstGlance, OCA, RCSB, PDBsum

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

Prokaryotes can use a variety of sugars as carbon sources in order to provide a selective survival advantage. The gene z5688 found in the pathogenic Escherichia coli O157:H7 encodes a "hypothetical" protein of unknown function. Sequence analysis identified the gene product as a putative member of the cupin superfamily of proteins, but no other functional information was known. We have determined the crystal structure of the Z5688 protein at 1.6 A resolution and identified the protein as a novel E. coli sugar isomerase (EcSI) through overall fold analysis and secondary-structure matching. Extensive substrate screening revealed that EcSI is capable of acting on d-lyxose and d-mannose. The complex structure of EcSI with fructose allowed the identification of key active-site residues, and mutagenesis confirmed their importance. The structure of EcSI also suggested a novel mechanism for substrate binding and product release in a cupin sugar isomerase. Supplementation of a nonpathogenic E. coli strain with EcSI enabled cell growth on the rare pentose d-lyxose.

Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli O157:H7.,van Staalduinen LM, Park CS, Yeom SJ, Adams-Cioaba MA, Oh DK, Jia Z J Mol Biol. 2010 Sep 3;401(5):866-81. Epub 2010 Jul 6. PMID:20615418[1]

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

References

  1. ↑ van Staalduinen LM, Park CS, Yeom SJ, Adams-Cioaba MA, Oh DK, Jia Z. Structure-based annotation of a novel sugar isomerase from the pathogenic E. coli O157:H7. J Mol Biol. 2010 Sep 3;401(5):866-81. Epub 2010 Jul 6. PMID:20615418 doi:10.1016/j.jmb.2010.06.063

3mpb, resolution 1.91Å

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