5CTM | pdb_00005ctm

Structure of BPu1 beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 
    0.138 (Depositor), 0.140 (DCC) 
  • R-Value Work: 
    0.126 (Depositor), 0.127 (DCC) 
  • R-Value Observed: 
    0.127 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Class D beta-lactamases do exist in Gram-positive bacteria.

Toth, M.Antunes, N.T.Stewart, N.K.Frase, H.Bhattacharya, M.Smith, C.A.Vakulenko, S.B.

(2016) Nat Chem Biol 12: 9-14

  • DOI: https://doi.org/10.1038/nchembio.1950
  • Primary Citation Related Structures: 
    5CTM, 5CTN

  • PubMed Abstract: 

    Production of β-lactamases of one of four molecular classes (A, B, C and D) is the major mechanism of bacterial resistance to β-lactams, the largest class of antibiotics, which have saved countless lives since their inception 70 years ago. Although several hundred efficient class D enzymes have been identified in Gram-negative pathogens over the last four decades, none have been reported in Gram-positive bacteria. Here we demonstrate that efficient class D β-lactamases capable of hydrolyzing a wide array of β-lactam substrates are widely disseminated in various species of environmental Gram-positive organisms. Class D enzymes of Gram-positive bacteria have a distinct structural architecture and employ a unique substrate-binding mode that is quite different from that of all currently known class A, C and D β-lactamases. These enzymes thus constitute a previously unknown reservoir of novel antibiotic-resistance enzymes.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.

Macromolecule Content 

  • Total Structure Weight: 55.48 kDa 
  • Atom Count: 4,904 
  • Modeled Residue Count: 465 
  • Deposited Residue Count: 466 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
233Bacillus pumilusMutation(s): 0 
Gene Names: BPUM_2340
EC: 3.5.2.6
UniProt
Find proteins for A8FFI9 (Bacillus pumilus (strain SAFR-032))
Explore A8FFI9 
Go to UniProtKB:  A8FFI9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8FFI9
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free:  0.138 (Depositor), 0.140 (DCC) 
  • R-Value Work:  0.126 (Depositor), 0.127 (DCC) 
  • R-Value Observed: 0.127 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.66α = 90
b = 79.87β = 92.29
c = 65.01γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-30
    Changes: Database references
  • Version 1.2: 2025-04-02
    Changes: Data collection, Database references, Derived calculations, Structure summary