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

    Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, California, USA.,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