Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.62 kDa 
• Atom Count: 4422 
• Modelled Residue Count: 530 
• Deposited Residue Count: 544 
• Unique protein chains: 1

5AEB

Crystal structure of the class B3 di-zinc metallo-beta-lactamase LRA- 12 from an Alaskan soil metagenome.

• PDB DOI: 10.2210/pdb5AEB/pdb

• Classification: HYDROLASE
• Organism(s): uncultured bacterium BLR12
• Mutation(s): No 


• Deposited: 2015-08-27 Released: 2015-09-16 
• Deposition Author(s): Power, P., Herman, R., Kerff, F., Bouillenne, F., Rodriguez, M.M., Galleni, M., Handelsman, J., Gutkind, G., Charlier, P., Sauvage, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Literature

Crystal structure and kinetic analysis of the class B3 di-zinc metallo-beta-lactamase LRA-12 from an Alaskan soil metagenome.

Rodriguez, M.M., Herman, R., Ghiglione, B., Kerff, F., D'Amico Gonzalez, G., Bouillenne, F., Galleni, M., Handelsman, J., Charlier, P., Gutkind, G., Sauvage, E., Power, P.

(2017) PLoS One 12: e0182043-e0182043

• PubMed: 28750094 
• DOI: 10.1371/journal.pone.0182043
• Primary Citation of Related Structures:  
  5AEB


• PubMed Abstract: 
  

We analyzed the kinetic properties of the metagenomic class B3 β-lactamase LRA-12, and determined its crystallographic structure in order to compare it with prevalent metallo-β-lactamases (MBLs) associated with clinical pathogens. We showed that LRA-12 confers extended-spectrum resistance on E. coli when expressed from recombinant clones, and the MIC values for carbapenems were similar to those observed in enterobacteria expressing plasmid-borne MBLs such as VIM, IMP or NDM. This was in agreement with the strong carbapenemase activity displayed by LRA-12, similar to GOB β-lactamases. Among the chelating agents evaluated, dipicolinic acid inhibited the enzyme more strongly than EDTA, which required pre-incubation with the enzyme to achieve measurable inhibition. Structurally, LRA-12 contains the conserved main structural features of di-zinc class B β-lactamases, and presents unique structural signatures that differentiate this enzyme from others within the family: (i) two loops (α3-β7 and β11-α5) that could influence antibiotic entrance and remodeling of the active site cavity; (ii) a voluminous catalytic cavity probably responsible for the high hydrolytic efficiency of the enzyme; (iii) the absence of disulfide bridges; (iv) a unique Gln116 at metal-binding site 1; (v) a methionine residue at position 221that replaces Cys/Ser found in other B3 β-lactamases in a predominantly hydrophobic environment, likely playing a role in protein stability. The structure of LRA-12 indicates that MBLs exist in wild microbial populations in extreme environments, or environments with low anthropic impact, and under the appropriate antibiotic selective pressure could be captured and disseminated to pathogens.

---

Organizational Affiliation: 

Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LRA-12	A, B	272	uncultured bacterium BLR12	Mutation(s): 0  Gene Names: blaLRA-12, AKSOIL_0006 EC: 3.5.2.6
UniProt
Find proteins for B5L5V5 (uncultured bacterium BLR12) Explore B5L5V5  Go to UniProtKB:  B5L5V5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], J [auth B], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO	G [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.235 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.148	α = 90
b = 80.616	β = 98.83
c = 78.288	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-08-27 
• Released Date: 2015-09-16 
Deposition Author(s): Power, P., Herman, R., Kerff, F., Bouillenne, F., Rodriguez, M.M., Galleni, M., Handelsman, J., Gutkind, G., Charlier, P., Sauvage, E.

Revision History  

• Version 1.0: 2015-09-16
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Database references