2dyu: Difference between revisions
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==Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad== | ==Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad== | ||
<StructureSection load='2dyu' size='340' side='right' caption='[[2dyu]], [[Resolution|resolution]] 1.75Å' scene=''> | <StructureSection load='2dyu' size='340' side='right'caption='[[2dyu]], [[Resolution|resolution]] 1.75Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2dyu]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2dyu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_pylori Campylobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DYU FirstGlance]. <br> | ||
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2dyv|2dyv]], [[2e2k|2e2k]], [[2e2l|2e2l]]</td></tr> | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dyv|2dyv]], [[2e2k|2e2k]], [[2e2l|2e2l]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">amiF ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">amiF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=85962 Campylobacter pylori])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Formamidase Formamidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.49 3.5.1.49] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dyu OCA], [https://pdbe.org/2dyu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dyu RCSB], [https://www.ebi.ac.uk/pdbsum/2dyu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dyu ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[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> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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[[Category: Campylobacter pylori]] | [[Category: Campylobacter pylori]] | ||
[[Category: Formamidase]] | [[Category: Formamidase]] | ||
[[Category: Large Structures]] | |||
[[Category: Hung, C L]] | [[Category: Hung, C L]] | ||
[[Category: Wang, W C]] | [[Category: Wang, W C]] | ||
Revision as of 14:41, 10 February 2021
Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triadHelicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad
Structural highlights
Function[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.[1] 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 PubMedHelicobacter 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. 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[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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