3KNR | pdb_00003knr

Bacillus cereus metallo-beta-lactamase Cys221Asp mutant, 1 mM Zn(II)

PDB DOI: https://doi.org/10.2210/pdb3KNR/pdb

Classification: HYDROLASE
Organism(s): Bacillus cereus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2009-11-12 Released: 2010-11-24
Deposition Author(s): Medrano Martin, F.J., Gonzalez, J.M., Vila, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.210 (Depositor), 0.206 (DCC)
R-Value Work:
0.172 (Depositor), 0.173 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Metallo-beta-lactamases withstand low Zn(II) conditions by tuning metal-ligand interactions.

Gonzalez, J.M., Meini, M.R., Tomatis, P.E., Medrano Martin, F.J., Cricco, J.A., Vila, A.J.

(2012) Nat Chem Biol 8: 698-700

PubMed: 22729148 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nchembio.1005
Primary Citation Related Structures:
3KNR, 3KNS

PubMed Abstract:
A number of multiresistant bacterial pathogens inactivate antibiotics by producing Zn(II)-dependent β-lactamases. We show that metal uptake leading to an active dinuclear enzyme in the periplasmic space of Gram-negative bacteria is ensured by a cysteine residue, an unusual metal ligand in oxidizing environments. Kinetic, structural and affinity data show that such Zn(II)-cysteine interaction is an adaptive trait that tunes the metal binding affinity, thus enabling antibiotic resistance at restrictive Zn(II) concentrations.

Organizational Affiliation

Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.

Macromolecule Content

Total Structure Weight: 101.23 kDa
Atom Count: 7,756
Modeled Residue Count: 837
Deposited Residue Count: 908
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase 2	A, B, C, D	227	Bacillus cereus	Mutation(s): 1 Gene Names: blm EC: 3.5.2.6
UniProt
Find proteins for P04190 (Bacillus cereus) Explore P04190 Go to UniProtKB: P04190
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04190
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	G [auth A], N [auth C], O [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth C] Focus chain O [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain Q [auth D] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A], J [auth A], P [auth C], Q [auth D], S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain R [auth D] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A] F [auth A] K [auth B] L [auth C] M [auth C] E [auth A], F [auth A], K [auth B], L [auth C], M [auth C], R [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain R [auth D]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]