4EUC

Succinyl-CoA:acetate CoA-transferase (AarCH6-E294A) in complex with dethiaacetyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.644 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structures of Acetobacter aceti Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase Reveal Specificity Determinants and Illustrate the Mechanism Used by Class I CoA-Transferases.

Mullins, E.A.Kappock, T.J.

(2012) Biochemistry 51: 8422-8434

  • DOI: 10.1021/bi300957f
  • Primary Citation of Related Structures:  4EU3, 4EU4, 4EU5, 4EU6, 4EU7, 4EU8, 4EU9, 4EUA, 4EUB, 4EUD
  • Also Cited By: 5DDK, 5DW4, 5DW5, 5DW6, 5E5H

  • PubMed Abstract: 
  • Coenzyme A (CoA)-transferases catalyze transthioesterification reactions involving acyl-CoA substrates, using an active-site carboxylate to form covalent acyl anhydride and CoA thioester adducts. Mechanistic studies of class I CoA-transferases sugges ...

    Coenzyme A (CoA)-transferases catalyze transthioesterification reactions involving acyl-CoA substrates, using an active-site carboxylate to form covalent acyl anhydride and CoA thioester adducts. Mechanistic studies of class I CoA-transferases suggested that acyl-CoA binding energy is used to accelerate rate-limiting acyl transfers by compressing the substrate thioester tightly against the catalytic glutamate [White, H., and Jencks, W. P. (1976) J. Biol. Chem. 251, 1688-1699]. The class I CoA-transferase succinyl-CoA:acetate CoA-transferase is an acetic acid resistance factor (AarC) with a role in a variant citric acid cycle in Acetobacter aceti. In an effort to identify residues involved in substrate recognition, X-ray crystal structures of a C-terminally His(6)-tagged form (AarCH6) were determined for several wild-type and mutant complexes, including freeze-trapped acetylglutamyl anhydride and glutamyl-CoA thioester adducts. The latter shows the acetate product bound to an auxiliary site that is required for efficient carboxylate substrate recognition. A mutant in which the catalytic glutamate was changed to an alanine crystallized in a closed complex containing dethiaacetyl-CoA, which adopts an unusual curled conformation. A model of the acetyl-CoA Michaelis complex demonstrates the compression anticipated four decades ago by Jencks and reveals that the nucleophilic glutamate is held at a near-ideal angle for attack as the thioester oxygen is forced into an oxyanion hole composed of Gly388 NH and CoA N2″. CoA is nearly immobile along its entire length during all stages of the enzyme reaction. Spatial and sequence conservation of key residues indicates that this mechanism is general among class I CoA-transferases.


    Related Citations: 
    • A specialized citric acid cycle requiring succinyl-coenzyme A (CoA):acetate CoA-transferase (AarC) confers acetic acid resistance on the acidophile Acetobacter aceti
      Mullins, E.A.,Francois, J.A.,Kappock, T.J.
      (2008) J.Bacteriol. 190: 4933


    Organizational Affiliation

    Department of Biochemistry, Purdue University, West Lafayette, IN 47907-2063, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinyl-CoA:acetate coenzyme A transferase
A, B
514Acetobacter acetiEC: 2.8.3.18
Find proteins for B3EY95 (Acetobacter aceti)
Go to UniProtKB:  B3EY95
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
0RQ
Query on 0RQ

Download SDF File 
Download CCD File 
A, B
[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3R)-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(4-oxidanylidenepentylamino)propyl]amino]butyl] hydrogen phosphate
dethiaacetyl-coenzyme A
C24 H40 N7 O17 P3
ZYXBXYCDXPIBJY-NDZSKPAWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0RQKd: 800 nM PDBBIND
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 79.490α = 90.00
b = 104.052β = 90.00
c = 120.134γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHENIXphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2012-11-07
    Type: Database references
  • Version 1.2: 2016-06-08
    Type: Other
  • Version 1.3: 2017-11-15
    Type: Refinement description