5WCK

Native FEZ-1 metallo-beta-lactamase from Legionella gormanii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:1K07


Literature

Three-dimensional structure of FEZ-1, a monomeric subclass B3 metallo-beta-lactamase from Fluoribacter gormanii, in native form and in complex with D-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: 10.1016/s0022-2836(02)01271-8
  • Primary Citation of Related Structures:  
    5W90, 5WCK, 1L9Y, 1K07, 1JT1

  • 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 ...

    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.


    Related Citations: 
    • A close look onto structural models and primary ligands of metallo-beta-lactamases.
      Raczynska, J.E., Shabalin, I.G., Minor, W., Wlodawer, A., Jaskolski, M.
      (2018) Drug Resist Updat 40: 1

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FEZ-1 proteinA, B263Fluoribacter gormaniiMutation(s): 2 
Gene Names: blaFEZ-1Lgor_2502NCTC11401_02334
EC: 3.5.2.6
UniProt
Find proteins for Q9K578 (Fluoribacter gormanii)
Explore Q9K578 
Go to UniProtKB:  Q9K578
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , H [auth A] , I [auth A] , J [auth A] , S [auth B] , T [auth B] , V [auth B] , 
E [auth A],  F [auth A],  H [auth A],  I [auth A],  J [auth A],  S [auth B],  T [auth B],  V [auth B],  W [auth B],  X [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A], U [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], Q [auth B], R [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , CA [auth B] , DA [auth B] , K [auth A] , L [auth A] , M [auth A] , N [auth A] , 
AA [auth B],  BA [auth B],  CA [auth B],  DA [auth B],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Y [auth B],  Z [auth B]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.158 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.86α = 90
b = 76.85β = 102.08
c = 78.89γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references