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''' | ||
==Overview== | |||
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. | |||
==About this Structure== | ==About this Structure== | ||
2DYU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | 2DYU 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=2DYU OCA]. | ||
==Reference== | |||
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] | |||
[[Category: Formamidase]] | [[Category: Formamidase]] | ||
[[Category: Helicobacter pylori]] | [[Category: Helicobacter pylori 26695]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Hung, C L.]] | [[Category: Hung, C L.]] | ||
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[[Category: Formamidase]] | [[Category: Formamidase]] | ||
[[Category: Helicobacter pylori]] | [[Category: Helicobacter pylori]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | [[Category: Hydrolase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 4 09:57:25 2008'' | |||
Revision as of 09:57, 4 June 2008
Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad
OverviewOverview
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.
About this StructureAbout this Structure
2DYU is a Single protein structure of sequence from Helicobacter pylori 26695. Full crystallographic information is available from OCA.
ReferenceReference
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 Page seeded by OCA on Wed Jun 4 09:57:25 2008