2e2k: Difference between revisions

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New page: left|200px<br /><applet load="2e2k" size="450" color="white" frame="true" align="right" spinBox="true" caption="2e2k, resolution 2.50Å" /> '''Helicobacter pylori ...
 
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[[Image:2e2k.gif|left|200px]]<br /><applet load="2e2k" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2e2k, resolution 2.50&Aring;" />
'''Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad'''<br />


==About this Structure==
==Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad==
2E2K is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Active as [http://en.wikipedia.org/wiki/Formamidase Formamidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.49 3.5.1.49] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2E2K OCA].
<StructureSection load='2e2k' size='340' side='right'caption='[[2e2k]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
[[Category: Formamidase]]
== Structural highlights ==
[[Category: Helicobacter pylori]]
<table><tr><td colspan='2'>[[2e2k]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E2K FirstGlance]. <br>
[[Category: Single protein]]
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
[[Category: Hung, C.L.]]
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e2k OCA], [https://pdbe.org/2e2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e2k RCSB], [https://www.ebi.ac.uk/pdbsum/2e2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e2k ProSAT]</span></td></tr>
[[Category: Wang, W.C.]]
</table>
[[Category: aliphatic amidase]]
== Function ==
[[Category: amif]]
[https://www.uniprot.org/uniprot/AMIF_HELPY AMIF_HELPY] Is an aliphatic amidase with a restricted substrate specificity, as it only hydrolyzes formamide. Probably involved in the nitrogen metabolism of H.pylori.<ref>PMID:11359566</ref>
[[Category: c166s]]
== Evolutionary Conservation ==
[[Category: catalytic triad]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: cek]]
Check<jmol>
[[Category: formamidase]]
  <jmolCheckbox>
[[Category: helicobacter pylori]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/2e2k_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=2e2k ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Helicobacter pylori AmiF formamidase that hydrolyzes formamide to produce formic acid and ammonia belongs to a member of the nitrilase superfamily. The crystal structure of AmiF was solved to 1.75A resolution using single-wavelength anomalous dispersion methods. The structure consists of a homohexamer related by 3-fold symmetry in which each subunit has an alpha-beta-beta-alpha four-layer architecture characteristic of the nitrilase superfamily. One exterior alpha layer faces the solvent, whereas the other one associates with that of the neighbor subunit, forming a tight alpha-beta-beta-alpha-alpha-beta-beta-alpha dimer. The apo and liganded crystal structures of an inactive mutant C166S were also determined to 2.50 and 2.30 A, respectively. These structures reveal a small formamide-binding pocket that includes Cys(166), Glu(60), and Lys(133) catalytic residues, in which Cys(166) acts as a nucleophile. Analysis of the liganded AmiF and N-carbamoyl d-amino acid amidohydrolase binding pockets reveals a common Cys-Glu-Lys triad, another conserved glutamate, and different subsets of ligand-binding residues. Molecular dynamic simulations show that the conserved triad has minimal fluctuations, catalyzing the hydrolysis of a specific nitrile or amide in the nitrilase superfamily efficiently.


''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:55:27 2007''
Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad.,Hung CL, Liu JH, Chiu WC, Huang SW, Hwang JK, Wang WC J Biol Chem. 2007 Apr 20;282(16):12220-9. Epub 2007 Feb 16. PMID:17307742<ref>PMID:17307742</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2e2k" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Helicobacter pylori 26695]]
[[Category: Large Structures]]
[[Category: Hung CL]]
[[Category: Wang WC]]
Retrieved from "https://proteopedia.org/2e2k"