1NIS

CRYSTAL STRUCTURE OF ACONITASE WITH TRANS-ACONITATE AND NITROCITRATE BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of aconitase with trans-aconitate and nitrocitrate bound.

Lauble, H.Kennedy, M.C.Beinert, H.Stout, C.D.

(1994) J.Mol.Biol. 237: 437-451

  • DOI: 10.1006/jmbi.1994.1246
  • Primary Citation of Related Structures:  1ACO, 1NIT

  • PubMed Abstract: 
  • Crystal structures of mitochondrial aconitase with the inhibitors trans-aconitate and nitrocitrate bound to the [4Fe-4S] cluster have been solved and refined at 2.05 A resolution with R-factors of 0.168 and 0.172, respectively. Crystallization of aco ...

    Crystal structures of mitochondrial aconitase with the inhibitors trans-aconitate and nitrocitrate bound to the [4Fe-4S] cluster have been solved and refined at 2.05 A resolution with R-factors of 0.168 and 0.172, respectively. Crystallization of aconitase with the substrates citrate and cis-aconitate has not been possible because the enzyme turns over and selects enzyme with isocitrate bound into the crystal lattice. Therefore we have analyzed crystal structures of the enzyme complexed with inhibitor analogs of these two substrates. The structure with nitrocitrate bound provides a model for citrate binding. The structure with trans-aconitate bound provides a model for cis-aconitate binding in two ways: Fe4 of the [4Fe-4S] cluster is five-coordinate and the carbon at the C beta position is trigonal. These results allow the model for the reaction mechanism to be extended to all three natural substrates of aconitase. The results support a model in which citrate and isocitrate form similar chelate structures related by 180 degrees rotation about the C alpha-C beta bond while the intermediate cis-aconitate binds in either of two ways (citrate mode or isocitrate mode). In both inhibitor complexes a H2O molecule is also bound to Fe4. In the structure with nitrocitrate bound, partial occupancy of sulfate in the active site is observed accompanied by hydroxyl binding to Fe4. Comparison of the structures with isocitrate, trans-aconitate, nitrocitrate and sulfate bound reveals preferred orientations for the three types of oxygens ligated to Fe4 (carboxyl, hydroxyl and H2O) supporting the proposed roles for His101, Asp165 and His167 in the catalytic mechanism.


    Related Citations: 
    • The Structure of Aconitase
      Robbins, A.H.,Stout, C.D.
      (1989) Proteins 5: 289
    • Structure of Activated Aconitase. Formation of the (4Fe-4S) Cluster in the Crystal
      Robbins, A.H.,Stout, C.D.
      (1989) Proc.Natl.Acad.Sci.USA 86: 3639
    • Iron-Sulfur Cluster in Aconitase. Crystallographic Evidence for a Three-Iron Center
      Robbins, A.H.,Stout, C.D.
      (1985) J.Biol.Chem. 260: 2328
    • Crystal Structure of Aconitase with Isocitrate and Nitroisocitrate Bound
      Lauble, H.,Kennedy, M.C.,Beinert, H.,Stout, C.D.
      (1992) Biochemistry 31: 2735


    Organizational Affiliation

    Department of Biochemistry, Medical College of Wisconsin, Milwaukee 53226.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACONITASE
A
754Bos taurusGene Names: ACO2
EC: 4.2.1.3
Find proteins for P20004 (Bos taurus)
Go to Gene View: ACO2
Go to UniProtKB:  P20004
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
NTC
Query on NTC

Download SDF File 
Download CCD File 
A
2-HYDROXY-2-NITROMETHYL SUCCINIC ACID
C5 H7 N O7
MTIGFRIXIPBOPZ-RXMQYKEDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Work: 0.172 
  • Space Group: B 1 1 2
Unit Cell:
Length (Å)Angle (°)
a = 185.500α = 90.00
b = 72.000β = 90.00
c = 73.000γ = 77.70
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other