6S0H

Structure of IMP-13 metallo-beta-lactamase complexed with hydrolysed doripenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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This is version 1.4 of the entry. See complete history


Literature

Structure and Molecular Recognition Mechanism of IMP-13 Metallo-beta-Lactamase.

Softley, C.A.Zak, K.M.Bostock, M.J.Fino, R.Zhou, R.X.Kolonko, M.Mejdi-Nitiu, R.Meyer, H.Sattler, M.Popowicz, G.M.

(2020) Antimicrob Agents Chemother 64

  • DOI: https://doi.org/10.1128/AAC.00123-20
  • Primary Citation of Related Structures:  
    6R73, 6R78, 6R79, 6RZR, 6RZS, 6S0H

  • PubMed Abstract: 

    Multidrug resistance among Gram-negative bacteria is a major global public health threat. Metallo-β-lactamases (MBLs) target the most widely used antibiotic class, the β-lactams, including the most recent generation of carbapenems. Interspecies spread renders these enzymes a serious clinical threat, and there are no clinically available inhibitors. We present the crystal structures of IMP-13, a structurally uncharacterized MBL from the Gram-negative bacterium Pseudomonas aeruginosa found in clinical outbreaks globally, and characterize the binding using solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The crystal structures of apo IMP-13 and IMP-13 bound to four clinically relevant carbapenem antibiotics (doripenem, ertapenem, imipenem, and meropenem) are presented. Active-site plasticity and the active-site loop, where a tryptophan residue stabilizes the antibiotic core scaffold, are essential to the substrate-binding mechanism. The conserved carbapenem scaffold plays the most significant role in IMP-13 binding, explaining the broad substrate specificity. The observed plasticity and substrate-locking mechanism provide opportunities for rational drug design of novel metallo-β-lactamase inhibitors, essential in the fight against antibiotic resistance.


  • Organizational Affiliation

    Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
227Pseudomonas aeruginosaMutation(s): 0 
Gene Names: bla-imp13bla-IMP13blaIMP-13
EC: 3.5.2.6
UniProt
Find proteins for Q7WYA8 (Pseudomonas aeruginosa)
Explore Q7WYA8 
Go to UniProtKB:  Q7WYA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7WYA8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KQ8 (Subject of Investigation/LOI)
Query on KQ8

Download Ideal Coordinates CCD File 
L [auth A],
P [auth B]
(2~{R},3~{R})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-methyl-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-2,3-dihydro-1~{H}-pyrrole-5-carboxylic acid
C15 H26 N4 O7 S2
DGCDKVKIMXIBKA-ZBJKAAEASA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
N [auth B],
O [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.43α = 90
b = 72.318β = 111.72
c = 62.933γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionGermany675555
German Federal Ministry for Education and ResearchGermanyGFTARV38
Polish National Science CentrePoland2018/28/T/NZ1/00337

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Structure summary
  • Version 1.2: 2020-04-29
    Changes: Database references
  • Version 1.3: 2020-06-03
    Changes: Database references
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references, Derived calculations