2e2k

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{{Seed}}
 
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[[Image:2e2k.png|left|200px]]
 
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==Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad==
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The line below this paragraph, containing "STRUCTURE_2e2k", creates the "Structure Box" on the page.
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<StructureSection load='2e2k' size='340' side='right'caption='[[2e2k]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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<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>
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{{STRUCTURE_2e2k| PDB=2e2k | SCENE= }}
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e2/2e2k_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_17307742}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2e2k" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 17307742 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17307742}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2E2K is a [[Single protein]] structure of sequence from [http://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].
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17307742 17307742]
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[[Category: Formamidase]]
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[[Category: Helicobacter pylori 26695]]
[[Category: Helicobacter pylori 26695]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Hung, C L.]]
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[[Category: Hung CL]]
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[[Category: Wang, W C.]]
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[[Category: Wang WC]]
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[[Category: Aliphatic amidase]]
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[[Category: Amif]]
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[[Category: C166]]
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[[Category: Catalytic triad]]
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[[Category: Cek]]
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[[Category: Formamidase]]
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[[Category: Helicobacter pylori]]
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[[Category: Hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 21:02:52 2008''
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Current revision

Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad

PDB ID 2e2k

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