2G2O

Structure of E.coli FabD complexed with sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mapping the active site of Escherichia coli malonyl-CoA-acyl carrier protein transacylase (FabD) by protein crystallography.

Oefner, C.Schulz, H.D'Arcy, A.Dale, G.E.

(2006) Acta Crystallogr D Biol Crystallogr 62: 613-618

  • DOI: https://doi.org/10.1107/S0907444906009474
  • Primary Citation of Related Structures:  
    2G1H, 2G2O, 2G2Y, 2G2Z

  • PubMed Abstract: 

    Malonyl-CoA-acyl carrier protein transacylase (FabD; EC 2.3.1.39) is a key enzyme in the fatty-acid biosynthesis pathway of bacteria, catalyzing the transfer of a malonyl moiety from malonyl-CoA to holo acyl carrier protein (ACP), generating malonyl-ACP and free CoASH. Malonyl-ACP, which is the product of this reaction, is the key building block for de novo fatty-acid biosynthesis. Various binary complex structures of the Escherichia coli enzyme are presented, including that of the natural substrate malonyl-CoA, indicating the functional role of the highly conserved amino acids Gln11, Ser92, Arg117 and His201 and the stabilizing function of the preformed oxyanion hole during the enzymatic reaction. Based on the presented structural data, a possible new catalytic enzyme mechanism is discussed. The data obtained could be used in aiding the process of rational inhibitor design.


  • Organizational Affiliation

    Morphochem AG, Basel, Switzerland. coefner@arpida.ch


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malonyl CoA-acyl carrier protein transacylase308Escherichia coli K-12Mutation(s): 0 
Gene Names: fabD
EC: 2.3.1.39
UniProt
Find proteins for P0AAI9 (Escherichia coli (strain K12))
Explore P0AAI9 
Go to UniProtKB:  P0AAI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AAI9
Sequence Annotations
Expand
  • 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: 1.76 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.109α = 90
b = 83.109β = 90
c = 164.237γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2006-05-30 
  • Deposition Author(s): Oefner, C.

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-30
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations