2BZ3

Structure of E.coli KAS I H298E mutant in complex with C12 fatty acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fatty acid synthesis. Role of active site histidines and lysine in Cys-His-His-type beta-ketoacyl-acyl carrier protein synthases.

von Wettstein-Knowles, P.Olsen, J.G.McGuire, K.A.Henriksen, A.

(2006) FEBS J. 273: 695-710

  • DOI: 10.1111/j.1742-4658.2005.05101.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Beta-ketoacyl-acyl carrier protein (ACP) synthase enzymes join short carbon units to construct fatty acyl chains by a three-step Claisen condensation reaction. The reaction starts with a trans thioesterification of the acyl primer substrate from ACP ...

    Beta-ketoacyl-acyl carrier protein (ACP) synthase enzymes join short carbon units to construct fatty acyl chains by a three-step Claisen condensation reaction. The reaction starts with a trans thioesterification of the acyl primer substrate from ACP to the enzyme. Subsequently, the donor substrate malonyl-ACP is decarboxylated to form a carbanion intermediate, which in the third step attacks C1 of the primer substrate giving rise to an elongated acyl chain. A subgroup of beta-ketoacyl-ACP synthases, including mitochondrial beta-ketoacyl-ACP synthase, bacterial plus plastid beta-ketoacyl-ACP synthases I and II, and a domain of human fatty acid synthase, have a Cys-His-His triad and also a completely conserved Lys in the active site. To examine the role of these residues in catalysis, H298Q, H298E and six K328 mutants of Escherichia colibeta-ketoacyl-ACP synthase I were constructed and their ability to carry out the trans thioesterification, decarboxylation and/or condensation steps of the reaction was ascertained. The crystal structures of wild-type and eight mutant enzymes with and/or without bound substrate were determined. The H298E enzyme shows residual decarboxylase activity in the pH range 6-8, whereas the H298Q enzyme appears to be completely decarboxylation deficient, showing that H298 serves as a catalytic base in the decarboxylation step. Lys328 has a dual role in catalysis: its charge influences acyl transfer to the active site Cys, and the steric restraint imposed on H333 is of critical importance for decarboxylation activity. This restraint makes H333 an obligate hydrogen bond donor at Nepsilon, directed only towards the active site and malonyl-ACP binding area in the fatty acid complex.


    Related Citations: 
    • Beta-Ketoacyl-(Acyl Carrier Protein) Synthase I of Escherichia Coli: Aspects of the Condensation Mechanism Revealed by Analyses of Mutations in the Active Site Pocket
      Mcguire, K.A.,Siggaard-Andersen, M.,Bangera, M.G.,Olsen, J.G.,von Wettstein-Knowles, P.
      (2001) Biochemistry 40: 9836
    • The X-Ray Crystal Structure of Beta-Ketoacyl (Acyl Carrier Protein) Synthase I
      Olsen, J.G.,Kadziola, A.,von Wettstein-Knowles, P.,Siggaard-Andersen, M.,Lindquist, Y.,Larsen, S.
      (1999) FEBS Lett. 460: 46
    • Structures of Beta-Ketoacyl-Acyl Carrier Protein Synthase I Complexed with Fatty Acids Elucidate its Catalytic Machinery
      Olsen, J.G.,Kadziola, A.,von Wettstein-Knowles, P.,Siggaard-Andersen, M.,Lindquist, Y.,Larsen, S.
      (2001) Structure 9: 233


    Organizational Affiliation

    Genetics Department, Molecular Biology and Physiology Institute, Copenhagen University, Denmark. knowles@biobase.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
A, B, C, D
418Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: fabB (fabC)
EC: 2.3.1.41
Find proteins for P0A953 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A953
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NH4
Query on NH4

Download SDF File 
Download CCD File 
A, C, D
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
DAO
Query on DAO

Download SDF File 
Download CCD File 
A, B, C, D
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.137α = 90.00
b = 139.171β = 90.00
c = 212.723γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-01
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2018-01-17
    Type: Data collection, Database references