1E25 | pdb_00001e25

The high resolution structure of PER-1 class A beta-lactamase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.183 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.140 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 
    0.140 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1E25

This is version 1.3 of the entry. See complete history

Literature

The High Resolution Crystal Structure for Class a Beta-Lactamase Per-1 Reveals the Bases for its Increase in Breadth of Activity

Tranier, S.Bouthors, A.T.Maveyraud, L.Guillet, V.Sougakoff, W.Samama, J.P.

(2000) J Biological Chem 275: 28075

  • DOI: https://doi.org/10.1074/jbc.M003802200
  • Primary Citation Related Structures: 
    1E25

  • PubMed Abstract: 

    The treatment of infectious diseases by beta-lactam antibiotics is continuously challenged by the emergence and dissemination of new beta-lactamases. In most cases, the cephalosporinase activity of class A enzymes results from a few mutations in the TEM and SHV penicillinases. The PER-1 beta-lactamase was characterized as a class A enzyme displaying a cephalosporinase activity. This activity was, however, insensitive to the mutations of residues known to be critical for providing extended substrate profiles to TEM and SHV. The x-ray structure of the protein, solved at 1.9-A resolution, reveals that two of the most conserved features in class A beta-lactamases are not present in this enzyme: the fold of the Omega-loop and the cis conformation of the peptide bond between residues 166 and 167. The new fold of the Omega-loop and the insertion of four residues at the edge of strand S3 generate a broad cavity that may easily accommodate the bulky substituents of cephalosporin substrates. The trans conformation of the 166-167 bond is related to the presence of an aspartic acid at position 136. Selection of class A enzymes based on the occurrence of both Asp(136) and Asn(179) identifies a subgroup of enzymes with high sequence homology.


  • Organizational Affiliation
    • Groupe de Cristallographie Biologique, Institut de Pharmacologie et de Biologie Structurale du CNRS, 205 route de Narbonne, F-31077 Toulouse cedex, France.

Macromolecule Content 

  • Total Structure Weight: 31.04 kDa 
  • Atom Count: 2,367 
  • Modeled Residue Count: 278 
  • Deposited Residue Count: 282 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
EXTENDED-SPECTRUM BETA-LACTAMASE PER-1282Pseudomonas aeruginosaMutation(s): 0 
Gene Names: BLAPER-1
EC: 3.5.2.6
UniProt
Find proteins for P37321 (Pseudomonas aeruginosa)
Explore P37321 
Go to UniProtKB:  P37321
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37321
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.183 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.140 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 0.140 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.6α = 90
b = 84.6β = 90
c = 46.89γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CNSphasing
SHARPphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other