6CTS | pdb_00006cts

PROPOSED MECHANISM FOR THE CONDENSATION REACTION OF CITRATE SYNTHASE. 1.9-ANGSTROMS STRUCTURE OF THE TERNARY COMPLEX WITH OXALOACETATE AND CARBOXYMETHYL COENZYME A

• PDB DOI: https://doi.org/10.2210/pdb6CTS/pdb

• Classification: OXO-ACID-LYASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 1989-11-16 Released: 1990-10-15 
• Deposition Author(s): Karpusas, M., Branchaud, B., Remington, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Observed: 
  0.110 (Depositor) 

Literature

Proposed mechanism for the condensation reaction of citrate synthase: 1.9-A structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme A.

Karpusas, M., Branchaud, B., Remington, S.J.

(1990) Biochemistry 29: 2213-2219

• PubMed: 2337600 
• Primary Citation Related Structures: 
  5CTS, 6CTS


• PubMed Abstract: 
  

  The crystal structure of the ternary complex citrate synthase-oxaloacetate-carboxymethyl coenzyme A has been solved to a resolution of 1.9 A and refined to a conventional crystallographic R factor of 0.185. The structure resembles a proposed transition state of the condensation reaction and suggests that the condensation reaction proceeds through a neutral enol rather than an enolate intermediate. A mechanism for the condensation reaction is proposed which involves the participation of three key catalytic groups (Asp 375, His 274, and His 320) in two distinct steps. The proposed mechanism invokes concerted general acid-base catalysis twice to explain both the energetics of the reaction and the experimentally observed inversion of stereochemistry at the attacking carbon atom.

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Organizational Affiliation: 
• Institute of Molecular Biology, University of Oregon, Eugene 97403.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 48.25 kDa 
• Atom Count: 3,466 
• Modeled Residue Count: 429 
• Deposited Residue Count: 433 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CITRATE SYNTHASE	A	433	Gallus gallus	Mutation(s): 0  EC: 4.1.3.7 (PDB Primary Data), 2.3.3.1 (UniProt)
UniProt
Find proteins for P23007 (Gallus gallus) Explore P23007  Go to UniProtKB:  P23007

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIC	B [auth A]	CITRYL-THIOETHER-COENZYME *A C27 H44 N7 O21 P3 S VPFUWJMPUQBRCJ-QVYRMQCDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Observed: 0.110 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104	α = 90
b = 78.1	β = 78.9
c = 58.3	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1990-10-15 
Deposition Author(s): Karpusas, M., Branchaud, B., Remington, S.J.

Revision History  

• Version 1.0: 1990-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations