Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 298.56 kDa 
• Atom Count: 23521 
• Modelled Residue Count: 2533 
• Deposited Residue Count: 2616 
• Unique protein chains: 1

2H12

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

• PDB DOI: 10.2210/pdb2H12/pdb

• Classification: TRANSFERASE
• Organism(s): Acetobacter aceti
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-15 Released: 2006-09-26 
• Deposition Author(s): Starks, C.M., Kappock, T.J.

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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 

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

• PubMed: 17087502 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate synthase	A, B, C, D, E, F	436	Acetobacter aceti	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMX	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
OAA	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
SO4	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

Binding Affinity Annotations
ID	Source	Binding 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 = 170.66	α = 90
b = 125.69	β = 90
c = 150.59	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
JBluIce-EPICS	data collection
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-15 
• Released Date: 2006-09-26 
Deposition Author(s): Starks, C.M., Kappock, T.J.

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