5CTN

Structure of BPu1 beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


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: 10.1038/nchembio.1950
  • Primary Citation of Related Structures:  

  • 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 s ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A, B
233Bacillus pumilus (strain SAFR-032)Mutation(s): 0 
EC: 3.5.2.6
Find proteins for A8FFI9 (Bacillus pumilus (strain SAFR-032))
Go to UniProtKB:  A8FFI9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
5R7
Query on 5R7

Download SDF File 
Download CCD File 
A, B
(2~{S},3~{R})-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid
Doripenem(open form, pyrroline tautomer form 3, SP3 connection to Thio as R isomer)
C15 H26 N4 O6 S2
RBKUPZPTQNSPAV-QZOCKBNKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.802α = 90.00
b = 80.002β = 92.85
c = 64.949γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 1.1: 2015-12-30
    Type: Database references
  • Version 1.2: 2016-10-05
    Type: Non-polymer description