1JT1

FEZ-1 metallo-beta-lactamase from Legionella gormanii modelled with D-captopril


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.161 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Three-dimensional Structure of FEZ-1, a Monomeric Subclass B3 Metallo-[beta]-lactamase from Fluoribacter gormanii, in Native Form and in Complex with -Captopril

Garcia-Saez, I.Mercuri, P.S.Papamicael, C.Kahn, R.Frere, J.M.Galleni, M.Rossolini, G.M.Dideberg, O.

(2003) J Mol Biol 325: 651-660

  • DOI: https://doi.org/10.1016/s0022-2836(02)01271-8
  • Primary Citation of Related Structures:  
    1JT1, 1K07, 1L9Y, 5W90, 5WCK

  • PubMed Abstract: 

    The beta-lactamases are involved in bacterial resistance to penicillin and related compounds. Members of the metallo-enzyme class are now found in many pathogenic bacteria and are thus becoming of major clinical importance. The structures of the Zn-beta-lactamase from Fluoribacter gormanii (FEZ-1) in the native and in the complex form are reported here. FEZ-1 is a monomeric enzyme, which possesses two zinc-binding sites. These structures are discussed in comparison with those of the tetrameric L1 enzyme produced by Stenotrophomonas maltophilia. From this analysis, amino acids involved in the oligomerization of L1 are clearly identified. Despite the similarity in fold, the active site of FEZ-1 was found to be significantly different. Two residues, which were previously implicated in function, are not present in L1 or in FEZ-1. The broad-spectrum substrate profile of Zn-beta-lactamases arises from the rather wide active-site cleft, where various beta-lactam compounds can be accommodated.


  • Organizational Affiliation

    Institut de Biologie Structurale (CIP), Jean-Pierre Ebel (CNRS-CEA), 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FEZ-1, class B3 metallo-beta-lactamase263Fluoribacter gormaniiMutation(s): 0 
Gene Names: blaFEZ-1
EC: 3.5.2.6
UniProt
Find proteins for Q9K578 (Fluoribacter gormanii)
Explore Q9K578 
Go to UniProtKB:  Q9K578
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K578
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MCO
Query on MCO

Download Ideal Coordinates CCD File 
I [auth A]1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID
C9 H15 N O3 S
FAKRSMQSSFJEIM-RNFRBKRXSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
MCO PDBBind:  1JT1 Ki: 4.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.12α = 90
b = 76.775β = 110.21
c = 44.841γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2013-05-08
    Changes: Advisory
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description