3KNS

Bacillus cereus metallo-beta-lactamase Cys221Asp mutant, 20 mM Zn(II)

PDB DOI: https://doi.org/10.2210/pdb3KNS/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: 1.58 Å
R-Value Free: 0.194
R-Value Work: 0.161
R-Value Observed: 0.163

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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nchembio.1005
Primary Citation of 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: 101.76 kDa
Atom Count: 7,937
Modelled Residue Count: 837
Deposited Residue Count: 908
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 H [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth D]	G [auth A], H [auth A], I [auth A], Q [auth B], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Focus chain Y [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A]	K [auth A], L [auth A], M [auth A], N [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain O [auth B] SDF format, chain X [auth D] SDF format, chain E [auth A] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D]	E [auth A] F [auth A] O [auth B] P [auth B] T [auth C] E [auth A], F [auth A], O [auth B], P [auth B], T [auth C], U [auth C], W [auth D], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D]	AA [auth D] J [auth A] R [auth B] S [auth B] V [auth C] AA [auth D], J [auth A], R [auth B], S [auth B], V [auth C], Z [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth C] Focus chain Z [auth D]