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 

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
  • 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 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Citrate synthaseABCDEF436Acetobacter acetiMutation(s): 0 
Gene Names: aarA
EC: 2.3.3.1 (PDB Primary Data), 2.3.3.16 (UniProt)
Find proteins for P20901 (Acetobacter aceti)
Explore P20901 
Go to UniProtKB:  P20901
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMX
Query on CMX

Download CCD File 
A, B, C, D, E, F
CARBOXYMETHYLDETHIA COENZYME *A
C23 H38 N7 O18 P3
SKRDARVCOPFVCP-GRFIIANRSA-N
 Ligand Interaction
OAA
Query on OAA

Download CCD File 
A, B, C, D, E, F
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OAAKd:  21100   nM  Binding MOAD
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



Entry History 

Deposition Data

Revision History 

  • 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