5B3R

Crystal structure of metallo-beta-lactamase IMP-18 from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb5B3R/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-10 Released: 2017-02-15 
• Deposition Author(s): Shimizu-Ibuka, A., Ishii, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Structural and Mutagenic Analysis of Metallo-beta-Lactamase IMP-18

Furuyama, T., Nonomura, H., Ishii, Y., Hanson, N.D., Shimizu-Ibuka, A.

(2016) Antimicrob Agents Chemother 60: 5521-5526

• PubMed: 27381398 
• DOI: https://doi.org/10.1128/AAC.00985-16
• Primary Citation of Related Structures:  
  5B3R


• PubMed Abstract: 
  

  IMP-type metallo-β-lactamases (MBLs) are exogenous zinc metalloenzymes that hydrolyze a broad range of β-lactams, including carbapenems. Here we report the crystal structure of IMP-18, an MBL cloned from Pseudomonas aeruginosa, at 2.0-Å resolution. The overall structure of IMP-18 resembles that of IMP-1, with an αβ/βα "folded sandwich" configuration, but the loop that covers the active site has a distinct conformation. The relationship between IMP-18's loop conformation and its kinetic properties was investigated by replacing the amino acid residues that can affect the loop conformation (Lys44, Thr50, and Ile69) in IMP-18 with those occupying the corresponding positions in the well-described enzyme IMP-1. The replacement of Thr50 with Pro considerably modified IMP-18's kinetic properties, specifically those pertaining to meropenem, with the kcat/Km value increased by an order of magnitude. The results indicate that this is a key residue that defines the kinetic properties of IMP-type β-lactamases.

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Organizational Affiliation: 

Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 51.09 kDa 
• Atom Count: 3,576 
• Modelled Residue Count: 433 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMP-18	A, B	228	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: IMP-18, blaIMP-18, imp-18 EC: 3.5.2.6
UniProt
Find proteins for Q5U807 (Pseudomonas aeruginosa) Explore Q5U807  Go to UniProtKB:  Q5U807

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A], H [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.55	α = 90
b = 87.38	β = 90
c = 105.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Shimizu-Ibuka, A., Ishii, Y.

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations