1QCA

QUADRUPLE MUTANT Q92C, N146F, Y168F, I172V TYPE III CAT COMPLEXED WITH FUSIDIC ACID. CRYSTALS GROWN AT PH 6.3. X-RAY DATA COLLECTED AT ROOM TEMPERATURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Steroid recognition by chloramphenicol acetyltransferase: engineering and structural analysis of a high affinity fusidic acid binding site.

Murray, I.A.Cann, P.A.Day, P.J.Derrick, J.P.Sutcliffe, M.J.Shaw, W.V.Leslie, A.G.

(1995) J Mol Biol 254: 993-1005

  • DOI: 10.1006/jmbi.1995.0671
  • Primary Citation of Related Structures:  
    1QCA

  • PubMed Abstract: 
  • The antibiotic fusidic acid and certain closely related steroidal compounds are potent competitive inhibitors of the type I variant of chloramphenicol acetyltransferase (CATI). In the absence of crystallographic data for CATI, the structural determinants of steroid binding were identified by (1) construction in vitro of genes encoding chimaeric enzymes containing segments of CATI and the related type III variant (CATIII) and (2) site-directed mutagenesis of the gene encoding CATIII, followed by kinetic characterisation of the substituted variants ...

    The antibiotic fusidic acid and certain closely related steroidal compounds are potent competitive inhibitors of the type I variant of chloramphenicol acetyltransferase (CATI). In the absence of crystallographic data for CATI, the structural determinants of steroid binding were identified by (1) construction in vitro of genes encoding chimaeric enzymes containing segments of CATI and the related type III variant (CATIII) and (2) site-directed mutagenesis of the gene encoding CATIII, followed by kinetic characterisation of the substituted variants. Replacement of four residues of CATIII (Gln92, Asn146, Tyr168 and Ile172) by their equivalents from CATI yields an enzyme variant that is susceptible to competitive inhibition by fusidate with respect to chloramphenicol (Ki = 5.4 microM). The structure of the complex of fusidate and the Q92C/N146F/Y168F/I172V variant, determined at 2.2 A resolution by X-ray crystallography, reveals the inhibitor bound deep within the chloramphenicol binding site and in close proximity to the side-chain of His195, an essential catalytic residue. The aromatic side-chain of Phe146 provides a critical hydrophobic surface which interacts with non-polar substituents of the steroid. The remaining three substitutions act in concert both to maintain the appropriate orientation of Phe 146 and via additional interactions with the bound inhibitor. The substitution of Gln92 by Cys eliminates a critical hydrogen bond interaction which constrains a surface loop (residues 137 to 142) of wild-type CATIII which must move in order for fusidate to bind to the enzyme. Only two hydrogen bonds are observed in the CAT-fusidate complex, involving the 3-alpha-hydroxyl of the A-ring and both hydroxyl of Tyr25 and NE2 of His195, both of which are also involved in hydrogen bonds with substrate in the CATIII-chloramphenicol complex. In the acetyl transfer reaction catalysed by CAT, NE2, of His195 serves as a general base in the abstraction of a proton from the 3-hydroxyl of chloramphenicol as the first chemical step in catalysis. The structure of the CAT-inhibitor complex suggests that deprotonation of the 3-alpha-hydroxyl of bound fusidate by this mechanism could produce an oxyanion nucleophile analogous to that seen with chloramphenicol, but one which is incorrectly positioned to attack the thioester carbonyl of acetyl-CoA, accounting for the observed failure of CAT to acetylate fusidate.


    Related Citations: 
    • Chloramphenicol Acetyltransferase
      Shaw, W.V., Leslie, A.G.W.
      (1991) Annu Rev Biophys Biophys Chem 20: 363
    • Refined Crystal Structure of Type III Chloramphenicol Acetyltransferase at 1.75-Angstroms Resolution
      Leslie, A.G.W.
      (1990) J Mol Biol 213: 167
    • Structure of Chloramphenicol Acetyltransferase at 1.75-Angstroms Resolution
      Leslie, A.G.W., Moody, P.C.E., Shaw, W.V.
      (1988) Proc Natl Acad Sci U S A 85: 4133

    Organizational Affiliation

    Department of Biochemistry, University of Leicester, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TYPE III CHLORAMPHENICOL ACETYLTRANSFERASEA213Shigella flexneriMutation(s): 0 
EC: 2.3.1.28
UniProt
Find proteins for P00484 (Escherichia coli)
Explore P00484 
Go to UniProtKB:  P00484
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00484
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUA
Query on FUA

Download Ideal Coordinates CCD File 
D [auth A]FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FUA Binding MOAD:  1QCA Ki: 5400 (nM) from 1 assay(s)
PDBBind:  1QCA Ki: 5400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.174 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.81α = 90
b = 107.81β = 90
c = 124.13γ = 120
Software Package:
Software NamePurpose
PROLSQrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 1995-08-03 
  • Released Date: 1995-10-15 
  • Deposition Author(s): Leslie, A.G.W.

Revision History  (Full details and data files)

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance