2H12

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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: 10.1021/bi061083k
  • Primary Citation of Related Structures:  
    2H12

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Citrate synthase
A, B, C, D, E, F
A, B, C, D, E, F
436Acetobacter acetiMutation(s): 0 
Gene Names: aarA
EC: 2.3.3.1 (PDB Primary Data), 2.3.3.16 (UniProt)
UniProt
Find proteins for P20901 (Acetobacter aceti)
Explore P20901 
Go to UniProtKB:  P20901
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20901
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMX
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]
CARBOXYMETHYLDETHIA COENZYME *A
C23 H38 N7 O18 P3
SKRDARVCOPFVCP-GRFIIANRSA-N
 Ligand Interaction
OAA
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]
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
SO4
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]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
OAA Binding MOAD:  2H12 Kd: 2.11e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
  • Diffraction Data DOI: 10.15785/SBGRID/336 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.66α = 90
b = 125.69β = 90
c = 150.59γ = 90
Software Package:
Software NamePurpose
CNSrefinement
JBluIce-EPICSdata collection
d*TREKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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