1CSC

Structure of ternary complexes of citrate synthase with D-and L-malate: Mechanistic implications


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

1.9-A structures of ternary complexes of citrate synthase with D- and L-malate: mechanistic implications.

Karpusas, M.Holland, D.Remington, S.J.

(1991) Biochemistry 30: 6024-6031

  • Primary Citation of Related Structures:  2CSC, 3CSC, 4CSC

  • PubMed Abstract: 
  • The structures of four isomorphous crystals of ternary complexes of chicken heart citrate synthase with D- or L-malate and acetyl coenzyme A or carboxymethyl coenzyme A have been determined by X-ray crystallography and fully refined at 1.9-A resoluti ...

    The structures of four isomorphous crystals of ternary complexes of chicken heart citrate synthase with D- or L-malate and acetyl coenzyme A or carboxymethyl coenzyme A have been determined by X-ray crystallography and fully refined at 1.9-A resolution. The structures show that both L-malate and D-malate bind in a very similar way in the presence of acetylCoA and that the enzyme conformation is "closed". Hydrogen bond geometry is suggested to account for the difference in binding constants of the two stereoisomers. The structures suggest that steric hindrance can account for the observation that proton exchange of acetyl coenzyme A with solvent is catalyzed by citrate synthase in the presence of L-malate but not D-malate. The ternary complexes with malate reveal the mode of binding of the substrate acetylCoA in the ground state. The carbonyl oxygen of the acetyl group is hydrogen bonded to a water molecule and to histidine 274, allowing unambiguous identification of the orientation of this group. The structures support the hypothesis that carboxymethyl coenzyme A is a transition-state analogue for the enolization step of the reaction (Bayer et al., 1981) and additionally support proposed mechanisms for the condensation reaction (Karpusas et al., 1990; Alter et al., 1990).


    Related Citations: 
    • Crystal Structure Analysis and Molecular Model of a Complex of Citrate Synthase with Oxaloacetate and S-Acetonyl-Coenzymea
      Wiegand, G.,Remington, S.,Deisenhofer, J.,Huber, R.
      (1984) J.Mol.Biol. 174: 205
    • Crystal Structure Analysis of the Tetragonal Crystal Form and Preliminary Molecular Model of Pig-Heart Citrate Synthase
      Wiegand, G.,Kukla, D.,Scholze, H.,Jones, T.A.,Huber, R.
      (1979) Eur.J.Biochem. 93: 41
    • Primary Structure of Porcine Heart Citrate Synthase
      Bloxham, D.P.,Parmelee, D.C.,Kumar, S.,Wade, R.D.,Ericsson, L.H.,Neurath, H.,Walsh, K.A.,Titani, K.
      (1981) Proc.Natl.Acad.Sci.USA 78: 5381
    • Crystallographic Refinement and Atomic Models of Two Different Forms of Citrate Synthase at 2.7 And 1.7 Angstroms Resolution
      Remington, S.,Wiegand, G.,Huber, R.
      (1982) J.Mol.Biol. 158: 111


    Organizational Affiliation

    Institute of Molecular Biology, University of Oregon, Eugene 97403.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CITRATE SYNTHASE
A
433Gallus gallusGene Names: CS
EC: 2.3.3.1
Find proteins for P23007 (Gallus gallus)
Go to Gene View: CS
Go to UniProtKB:  P23007
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMC
Query on CMC

Download SDF File 
Download CCD File 
A
CARBOXYMETHYL COENZYME *A
C23 H38 N7 O18 P3 S
OBUOSIHPWVNVJN-GRFIIANRSA-N
 Ligand Interaction
LMR
Query on LMR

Download SDF File 
Download CCD File 
A
(2S)-2-hydroxybutanedioic acid
L-Malate
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.000α = 90.00
b = 78.100β = 78.90
c = 58.300γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-04-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other