2yz3

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[[Image:2yz3.jpg|left|200px]]
[[Image:2yz3.jpg|left|200px]]
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{{Structure
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<!--
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|PDB= 2yz3 |SIZE=350|CAPTION= <scene name='initialview01'>2yz3</scene>, resolution 2.30&Aring;
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The line below this paragraph, containing "STRUCTURE_2yz3", creates the "Structure Box" on the page.
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|SITE= <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+301'>AC1</scene>, <scene name='pdbsite=AC2:Zn+Binding+Site+For+Residue+A+302'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Residue+B+303'>AC3</scene>, <scene name='pdbsite=AC4:Zn+Binding+Site+For+Residue+B+304'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Residue+B+501'>AC5</scene>, <scene name='pdbsite=AC6:So4+Binding+Site+For+Residue+A+502'>AC6</scene>, <scene name='pdbsite=AC7:So4+Binding+Site+For+Residue+A+503'>AC7</scene>, <scene name='pdbsite=AC8:So4+Binding+Site+For+Residue+B+504'>AC8</scene>, <scene name='pdbsite=AC9:M5p+Binding+Site+For+Residue+A+401'>AC9</scene> and <scene name='pdbsite=BC1:M5p+Binding+Site+For+Residue+B+402'>BC1</scene>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=M5P:(S)-2-(MERCAPTOMETHYL)-5-PHENYLPENTANOIC+ACID'>M5P</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span>
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or leave the SCENE parameter empty for the default display.
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|GENE= VIM-2, bla VIM-2, blaVIM-2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida])
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-->
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|DOMAIN=
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{{STRUCTURE_2yz3| PDB=2yz3 | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yz3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yz3 OCA], [http://www.ebi.ac.uk/pdbsum/2yz3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2yz3 RCSB]</span>
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}}
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'''Crystallographic Investigation of Inhibition Mode of the VIM-2 Metallo-beta-lactamase from Pseudomonas aeruginosa with Mercaptocarboxylate Inhibitor'''
'''Crystallographic Investigation of Inhibition Mode of the VIM-2 Metallo-beta-lactamase from Pseudomonas aeruginosa with Mercaptocarboxylate Inhibitor'''
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[[Category: Yamagata, Y.]]
[[Category: Yamagata, Y.]]
[[Category: Yamaguchi, Y.]]
[[Category: Yamaguchi, Y.]]
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[[Category: enzyme-inhibitor complex]]
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[[Category: Enzyme-inhibitor complex]]
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[[Category: hydrolase]]
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[[Category: Hydrolase]]
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[[Category: metallo-beta-lactamase]]
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[[Category: Metallo-beta-lactamase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 19:43:17 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:16:43 2008''
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Revision as of 16:43, 4 May 2008

Image:2yz3.jpg

Template:STRUCTURE 2yz3

Crystallographic Investigation of Inhibition Mode of the VIM-2 Metallo-beta-lactamase from Pseudomonas aeruginosa with Mercaptocarboxylate Inhibitor


Overview

The VIM-2 metallo-beta-lactamase enzyme from Pseudomonas aeruginosa catalyzes the hydrolysis of most beta-lactam antibiotics including carbapenems, and there are currently no potent inhibitors of such enzymes. We found rac-2-omega-phenylpropyl-3-mercaptopropionic acid, phenylC3SH, to be a potent inhibitor of VIM-2. The structure of the VIM-2-phenylC3SH complex was determined by X-ray crystallography to 2.3 A. The structure revealed that the thiol group of phenylC3SH bridged to the two zinc(II) ions and the phenyl group interacted with Tyr67(47) on loop1 near the active site, by pi-pi stacking interactions. The methylene group interacted with Phe61(42) located at the bottom of loop1 through CH-pi interactions. Dynamic movements were observed in Arg228(185) and Asn233(190) on loop2, compared with the native structure (PDB code: 1KO3 ). These results suggest that the above-mentioned four residues play important roles in the binding and recognition of inhibitors or substrates and in stabilizing a loop in the VIM-2 enzyme.

About this Structure

2YZ3 is a Single protein structure of sequence from Pseudomonas putida. Full crystallographic information is available from OCA.

Reference

Crystallographic investigation of the inhibition mode of a VIM-2 metallo-beta-lactamase from Pseudomonas aeruginosa by a mercaptocarboxylate inhibitor., Yamaguchi Y, Jin W, Matsunaga K, Ikemizu S, Yamagata Y, Wachino J, Shibata N, Arakawa Y, Kurosaki H, J Med Chem. 2007 Dec 27;50(26):6647-53. Epub 2007 Dec 6. PMID:18052313 Page seeded by OCA on Sun May 4 19:43:17 2008

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