9GX8 | pdb_00009gx8

Crystal structure of CIM-2, a membrane-bound B1 metallo-beta-lactamase from Chryseobacterium indologenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.195 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9GX8

This is version 1.1 of the entry. See complete history

Literature

Active site loops of membrane-anchored metallo-beta-lactamases from environmental bacteria determine cephalosporinase activity.

Carnevale, M.C.Palacios, A.R.Hinchliffe, P.Delmonti, J.Drusin, S.I.Moreno, D.M.Bonomo, R.A.Spencer, J.Vila, A.J.

(2025) Antimicrob Agents Chemother 69: e0191824-e0191824

  • DOI: https://doi.org/10.1128/aac.01918-24
  • Primary Citation Related Structures: 
    9GX8, 9GX9

  • PubMed Abstract: 

    Antimicrobial resistance is a significant global public health threat that limits treatment options for bacterial infections. This situation is aggravated by the environmental spread of β-lactamase genes. In particular, metallo-β-lactamases (MBLs) hydrolyze almost all available β-lactam antibiotics, including late-generation cephalosporins and carbapenems. Among MBLs, the New Delhi metallo-β-lactamase (NDM-1) of subclass B1 has shown the most ominous dissemination. NDM variants are the only MBLs of clinical importance that are membrane-anchored, a sub-cellular localization that endows them with high stability under conditions of metal limitation. However, antibiotic resistance predates modern antibiotic usage, and environmental bacteria serve as reservoirs for resistance genes. Here, we report the biochemical and structural characterization of two membrane-bound MBLs: CJO-1 and CIM-2, from Chryseobacterium joostei and Chryseobacterium indologenes , respectively. Both MBLs confer β-lactam resistance on producer bacterial strains and hydrolyze several antibiotics, although with impaired efficiency compared to NDM-1. Crystal structures reveal differences, compared to previously studied B1 MBLs, in the active site loops and their dynamic properties that impact activity. Specifically, a hindered access to the active site with the contribution of a Tyr residue in loop L10 and the presence of a positively charged Lys residue in loop L3 limit hydrolysis of cephalosporins with charged C3 substituents. Some of these novel features are preserved in other MBLs from Chryseobacterium spp. These findings suggest that Chryseobacterium spp. could act as reservoirs of MBL genes, while informing on the diversity of structure-function relationships and dynamic behaviors within the B1 subclass of these enzymes.


  • Organizational Affiliation
    • Laboratorio de Metaloproteínas, Instituto de Biologia Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina.

Macromolecule Content 

  • Total Structure Weight: 52.53 kDa 
  • Atom Count: 4,122 
  • Modeled Residue Count: 448 
  • Deposited Residue Count: 464 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase type 2
A, B
232Chryseobacterium indologenesMutation(s): 0 
Gene Names: AOB46_06505
EC: 3.5.2.6
UniProt
Find proteins for A0A0N0IX17 (Chryseobacterium indologenes)
Explore A0A0N0IX17 
Go to UniProtKB:  A0A0N0IX17
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0N0IX17
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD

Query on MPD



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PGR

Query on PGR



Download:Ideal Coordinates CCD File
M [auth B]R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.195 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.287α = 90
b = 43.131β = 115.959
c = 75.691γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI100560

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references