3znb
From Proteopedia
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|PDB= 3znb |SIZE=350|CAPTION= <scene name='initialview01'>3znb</scene>, resolution 2.7Å | |PDB= 3znb |SIZE=350|CAPTION= <scene name='initialview01'>3znb</scene>, resolution 2.7Å | ||
|SITE= <scene name='pdbsite=HG:Zn2+Was+Ejected+And+The+Hg+Is+Bound+In+A+Different+Position'>HG</scene>, <scene name='pdbsite=NA:Deduced+From+The+Coordination+In+The+Native+Structure.+N+...'>NA</scene> and <scene name='pdbsite=ZN:The+Zn+Is+Located+In+The+Same+Position+As+Zn1+In+The+Nat+...'>ZN</scene> | |SITE= <scene name='pdbsite=HG:Zn2+Was+Ejected+And+The+Hg+Is+Bound+In+A+Different+Position'>HG</scene>, <scene name='pdbsite=NA:Deduced+From+The+Coordination+In+The+Native+Structure.+N+...'>NA</scene> and <scene name='pdbsite=ZN:The+Zn+Is+Located+In+The+Same+Position+As+Zn1+In+The+Nat+...'>ZN</scene> | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
| - | |ACTIVITY= [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] | + | |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> |
|GENE= CCRA3 (WITHOUT SIGNAL SEQUENCE) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 Bacteroides fragilis]) | |GENE= CCRA3 (WITHOUT SIGNAL SEQUENCE) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=817 Bacteroides fragilis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3znb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3znb OCA], [http://www.ebi.ac.uk/pdbsum/3znb PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3znb RCSB]</span> | ||
}} | }} | ||
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[[Category: Concha, N O.]] | [[Category: Concha, N O.]] | ||
[[Category: Herzberg, O.]] | [[Category: Herzberg, O.]] | ||
| - | [[Category: HG]] | ||
| - | [[Category: NA]] | ||
| - | [[Category: ZN]] | ||
[[Category: beta-lactamase]] | [[Category: beta-lactamase]] | ||
[[Category: hydrolase]] | [[Category: hydrolase]] | ||
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[[Category: zinc]] | [[Category: zinc]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:36:41 2008'' |
Revision as of 02:36, 31 March 2008
| |||||||
| , resolution 2.7Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , and | ||||||
| Ligands: | , , | ||||||
| Gene: | CCRA3 (WITHOUT SIGNAL SEQUENCE) (Bacteroides fragilis) | ||||||
| Activity: | Beta-lactamase, with EC number 3.5.2.6 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
METALLO-BETA-LACTAMASE (ZN, HG-BOUND FORM)
Overview
The metallo-beta-lactamases require zinc or cadmium for hydrolyzing beta-lactam antibiotics and are inhibited by mercurial compounds. To data, there are no clinically useful inhibitors of this class of enzymes. The crystal structure of the Zn(2+)-bound enzyme from Bacteroides fragilis contains a binuclear zinc center in the active site. A hydroxide, coordinated to both zinc atoms, is proposed as the moiety that mounts the nucleophilic attack on the carbonyl carbon atom of the beta-lactam ring. To study the metal coordination further, the crystal structures of a Cd(2+)-bound enzyme and of an Hg(2+)-soaked zinc-containing enzyme have been determined at 2.1 A and 2.7 A, respectively. Given the diffraction resolution, the Cd(2+)-bound enzyme exhibits the same active-site architecture as that of the Zn(2+)-bound enzyme, consistent with the fact that both forms are enzymatically active. The 10-fold reduction in activity of the Cd(2+)-bound molecule compared with the Zn(2+)-bound enzyme is attributed to fine differences in the charge distribution due to the difference in the ionic radii of the two metals. In contrast, in the Hg(2+)-bound structure, one of the zinc ions, Zn2, was ejected, and the other zinc ion, Zn1, remained in the same site as in the 2-Zn(2+)-bound structure. Instead of the ejected zinc, a mercury ion binds between Cys 104 and Cys 181, 4.8 A away from Zn1 and 3.9 A away from the site where Zn2 is located in the 2-Zn(2+)-bound molecule. The perturbed binuclear metal cluster explains the inactivation of the enzyme by mercury compounds.
About this Structure
3ZNB is a Single protein structure of sequence from Bacteroides fragilis. Full crystallographic information is available from OCA.
Reference
Crystal structures of the cadmium- and mercury-substituted metallo-beta-lactamase from Bacteroides fragilis., Concha NO, Rasmussen BA, Bush K, Herzberg O, Protein Sci. 1997 Dec;6(12):2671-6. PMID:9416622
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