1i78: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
New page: left|200px<br /><applet load="1i78" size="450" color="white" frame="true" align="right" spinBox="true" caption="1i78, resolution 2.6Å" /> '''CRYSTAL STRUCTURE OF ...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1i78.jpg|left|200px]]<br /><applet load="1i78" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1i78, resolution 2.6&Aring;" />
'''CRYSTAL STRUCTURE OF OUTER MEMBRANE PROTEASE OMPT FROM ESCHERICHIA COLI'''<br />


==Overview==
==CRYSTAL STRUCTURE OF OUTER MEMBRANE PROTEASE OMPT FROM ESCHERICHIA COLI==
OmpT from Escherichia coli belongs to a family of highly homologous outer, membrane proteases, known as omptins, which are implicated in the, virulence of several pathogenic Gram-negative bacteria. Here we present, the crystal structure of OmpT, which shows a 10-stranded antiparallel, beta-barrel that protrudes far from the lipid bilayer into the, extracellular space. We identified a putative binding site for, lipopolysaccharide, a molecule that is essential for OmpT activity. The, proteolytic site is located in a groove at the extracellular top of the, vase-shaped beta-barrel. Based on the constellation of active site, residues, we propose a novel proteolytic mechanism, involving a His-Asp, dyad and an Asp-Asp couple that activate a putative nucleophilic water, molecule. The active site is fully conserved within the omptin family., Therefore, the structure described here provides a sound basis for the, design of drugs against omptin-mediated bacterial pathogenesis., Coordinates are in the Protein Data Bank (accession No. 1I78)
<StructureSection load='1i78' size='340' side='right'caption='[[1i78]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1i78]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I78 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I78 FirstGlance]. <br>
1I78 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with BOG and MPD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Omptin Omptin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.49 3.4.23.49] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1I78 OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1i78 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i78 OCA], [https://pdbe.org/1i78 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i78 RCSB], [https://www.ebi.ac.uk/pdbsum/1i78 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i78 ProSAT]</span></td></tr>
Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site., Vandeputte-Rutten L, Kramer RA, Kroon J, Dekker N, Egmond MR, Gros P, EMBO J. 2001 Sep 17;20(18):5033-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11566868 11566868]
</table>
[[Category: Escherichia coli]]
== Function ==
[[Category: Omptin]]
[https://www.uniprot.org/uniprot/OMPT_ECOLI OMPT_ECOLI] Protease that can cleave T7 RNA polymerase, ferric enterobactin receptor protein (FEP), antimicrobial peptide protamine and other proteins. This protease has a specificity for paired basic residues.<ref>PMID:9683502</ref>
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Dekker, N.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Egmond, M.R.]]
Check<jmol>
[[Category: Gros, P.]]
  <jmolCheckbox>
[[Category: Kramer, R.A.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i7/1i78_consurf.spt"</scriptWhenChecked>
[[Category: Kroon, J.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Vandeputte-Rutten, L.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: BOG]]
  </jmolCheckbox>
[[Category: MPD]]
</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=1i78 ConSurf].
[[Category: beta barrel]]
<div style="clear:both"></div>
[[Category: integral outer membrane protein]]
== References ==
[[Category: protease]]
<references/>
 
__TOC__
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:07:07 2007''
</StructureSection>
[[Category: Escherichia coli K-12]]
[[Category: Large Structures]]
[[Category: Dekker N]]
[[Category: Egmond MR]]
[[Category: Gros P]]
[[Category: Kramer RA]]
[[Category: Kroon J]]
[[Category: Vandeputte-Rutten L]]
Retrieved from "https://proteopedia.org/1i78"