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 

wwPDB Validation 3D Report Full Report


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

  • 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 compo ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Citrate synthase
A, B, C, D, E, F
436Acetobacter acetiMutation(s): 0 
Gene Names: aarA
EC: 2.3.3.16
Find proteins for P20901 (Acetobacter aceti)
Go to UniProtKB:  P20901
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
OAA
Query on OAA

Download SDF File 
Download CCD File 
A, B, C, D, E, F
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
CMX
Query on CMX

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CARBOXYMETHYLDETHIA COENZYME *A
C23 H38 N7 O18 P3
SKRDARVCOPFVCP-GRFIIANRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OAAKd: 21100 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 170.660α = 90.00
b = 125.690β = 90.00
c = 150.590γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
JBluIce-EPICSdata collection
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2007-10-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description