5LS3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1002/anie.201612185
  • Primary Citation of Related Structures:  
    5LS3

  • 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 aeruginosa. Cysteinyl variants on the α3 and L3 regions, which flank the di-Zn II 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase IMP-1A [auth B],
B [auth A]
250Pseudomonas aeruginosaMutation(s): 1 
Gene Names: spm-1bla SPM-1blaSPM-1CCBH4851_00081ICEPaeSP_00028
EC: 3.5.2.6
UniProt
Find proteins for Q8G9Q0 (Pseudomonas aeruginosa)
Explore Q8G9Q0 
Go to UniProtKB:  Q8G9Q0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8G9Q0
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.886α = 90
b = 59.886β = 90
c = 276.115γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-03-29
    Changes: Database references
  • Version 1.2: 2017-07-12
    Changes: Structure summary
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description