5LS3

Crystal structure of metallo-beta-lactamase SPM-1 with Y58C mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.754 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

(19) F-NMR Reveals the Role of Mobile Loops in Product and Inhibitor Binding by the Sao Paulo Metallo-beta-Lactamase.

Abboud, M.I.Hinchliffe, P.Brem, J.Macsics, R.Pfeffer, I.Makena, A.Umland, K.D.Rydzik, A.M.Li, G.B.Spencer, J.Claridge, T.D.Schofield, C.J.

(2017) Angew. Chem. Int. Ed. Engl. 56: 3862-3866

  • DOI: 10.1002/anie.201612185

  • PubMed Abstract: 
  • Resistance to β-lactam antibiotics mediated by metallo-β-lactamases (MBLs) is a growing problem. We describe the use of protein-observe 19 F-NMR (PrOF NMR) to study the dynamics of the São Paulo MBL (SPM-1) from β-lactam-resistant Pseudomonas aerugin ...

    Resistance to β-lactam antibiotics mediated by metallo-β-lactamases (MBLs) is a growing problem. We describe the use of protein-observe 19 F-NMR (PrOF NMR) to study the dynamics of the São Paulo MBL (SPM-1) from β-lactam-resistant Pseudomonas aeruginosa. Cysteinyl variants on the α3 and L3 regions, which flank the di-ZnII active site, were selectively 19 F-labeled using 3-bromo-1,1,1-trifluoroacetone. The PrOF NMR results reveal roles for the mobile α3 and L3 regions in the binding of both inhibitors and hydrolyzed β-lactam products to SPM-1. These results have implications for the mechanisms and inhibition of MBLs by β-lactams and non-β-lactams and illustrate the utility of PrOF NMR for efficiently analyzing metal chelation, identifying new binding modes, and studying protein binding from a mixture of equilibrating isomers.


    Organizational Affiliation

    Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase IMP-1
B, A
250Pseudomonas aeruginosaMutation(s): 1 
Gene Names: spm-1 (bla SPM-1, blaSPM-1)
EC: 3.5.2.6
Find proteins for Q8G9Q0 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q8G9Q0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.754 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.886α = 90.00
b = 59.886β = 90.00
c = 276.115γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG1100135
ational Institute of Allergy and Infectious Diseases of the U.S. National Institutes of HealthUnited StatesR01AI100560

Revision History 

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Database references
  • Version 1.2: 2017-07-12
    Type: Structure summary
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence