Structure of Acetobacter aceti citrate synthase complexed with oxaloacetate and carboxymethyldethia coenzyme A (CMX)

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Structure of a NADH-insensitive hexameric citrate synthase that resists acid inactivation.

Francois, J.A.Starks, C.M.Sivanuntakorn, S.Jiang, H.Ransome, A.E.Nam, J.W.Constantine, C.Z.Kappock, T.J.

(2006) Biochemistry 45: 13487-13499

  • DOI: https://doi.org/10.1021/bi061083k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Acetobacter aceti converts ethanol to acetic acid, and strains highly resistant to both are used to make vinegar. A. aceti survives acetic acid exposure by tolerating cytoplasmic acidification, which implies an unusual adaptation of cytoplasmic components to acidic conditions. A. aceti citrate synthase (AaCS), a hexameric type II citrate synthase, is required for acetic acid resistance and, therefore, would be expected to function at low pH. Recombinant AaCS has intrinsic acid stability that may be a consequence of strong selective pressure to function at low pH, and unexpectedly high thermal stability for a protein that has evolved to function at approximately 30 degrees C. The crystal structure of AaCS, complexed with oxaloacetate (OAA) and the inhibitor carboxymethyldethia-coenzyme A (CMX), was determined to 1.85 A resolution using protein purified by a tandem affinity purification procedure. This is the first crystal structure of a "closed" type II CS, and its active site residues interact with OAA and CMX in the same manner observed in the corresponding type I chicken CS.OAA.CMX complex. While AaCS is not regulated by NADH, it retains many of the residues used by Escherichia coli CS (EcCS) for NADH binding. The surface of AaCS is abundantly decorated with basic side chains and has many fewer uncompensated acidic charges than EcCS; this constellation of charged residues is stable in varied pH environments and may be advantageous in the A. aceti cytoplasm.

  • Organizational Affiliation

    Department of Chemistry, Washington University, St. Louis, Missouri 63130-4899, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Citrate synthase
A, B, C, D, E
A, B, C, D, E, F
436Acetobacter acetiMutation(s): 0 
Gene Names: aarA
Find proteins for P20901 (Acetobacter aceti)
Explore P20901 
Go to UniProtKB:  P20901
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20901
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CMX

Download Ideal Coordinates CCD File 
GB [auth F]
HA [auth C]
O [auth A]
PA [auth D]
YA [auth E]
GB [auth F],
HA [auth C],
O [auth A],
PA [auth D],
YA [auth E],
Z [auth B]
C23 H38 N7 O18 P3
Query on OAA

Download Ideal Coordinates CCD File 
AA [auth C]
G [auth A]
IA [auth D]
P [auth B]
QA [auth E]
AA [auth C],
G [auth A],
IA [auth D],
P [auth B],
QA [auth E],
ZA [auth F]
C4 H3 O5
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth F]
BA [auth C]
BB [auth F]
CA [auth C]
CB [auth F]
AB [auth F],
BA [auth C],
BB [auth F],
CA [auth C],
CB [auth F],
DA [auth C],
DB [auth F],
EA [auth C],
EB [auth F],
FA [auth C],
FB [auth F],
GA [auth C],
H [auth A],
I [auth A],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
OA [auth D],
Q [auth B],
R [auth B],
RA [auth E],
S [auth B],
SA [auth E],
T [auth B],
TA [auth E],
U [auth B],
UA [auth E],
V [auth B],
VA [auth E],
W [auth B],
WA [auth E],
X [auth B],
XA [auth E],
Y [auth B]
O4 S
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.66α = 90
b = 125.69β = 90
c = 150.59γ = 90
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2007-10-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description