2G1H

Structure of E.coli FabD complexed with glycerol

• PDB DOI: https://doi.org/10.2210/pdb2G1H/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-02-14 Released: 2006-05-30 
• Deposition Author(s): Oefner, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.222 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

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

• PubMed: 16699188 
• 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.

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Organizational Affiliation: 

Morphochem AG, Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.4 kDa 
• Atom Count: 2,430 
• Modelled Residue Count: 307 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malonyl CoA-acyl carrier protein transacylase	A	308	Escherichia coli K-12	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.222 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.147	α = 90
b = 83.147	β = 90
c = 164.511	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description