1AMI

STERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Steric and conformational features of the aconitase mechanism.

Lauble, H.Stout, C.D.

(1995) Proteins 22: 1-11

  • DOI: 10.1002/prot.340220102
  • Primary Citation of Related Structures:  1AMJ

  • PubMed Abstract: 
  • Crystal structures of mitochondrial aconitase with alpha-methylisocitrate and with sulfate bound have been solved and refined at 2.0 A resolution with R factors of 18.2 and 16.8%, respectively. The steric factors and conformational effects observed i ...

    Crystal structures of mitochondrial aconitase with alpha-methylisocitrate and with sulfate bound have been solved and refined at 2.0 A resolution with R factors of 18.2 and 16.8%, respectively. The steric factors and conformational effects observed in both new structures support the proposed mechanism for the overall reaction catalyzed by aconitase. The alternate substrate alpha-methylisocitrate is derived from alpha-methyl-cis-aconitate during crystallization and is observed to bind in the active site in a manner very similar to that observed for isocitrate. The methyl group is accommodated by favorable contact with Ile-425. However, the other potential hydration product of alpha-methyl-cis-aconitate, alpha-methylcitrate, cannot be accommodated in the active site due to steric conflict of the methyl group with Asp-165. The results are consistent with the requirement that cis-aconitate must bind in two ways, in the citrate mode and in the isocitrate mode. Crystals of aconitase with sulfate bound are isomorphous to those with isocitrate bound. However, the structure displays significant conformational changes, providing a model for the substrate-free state of enzyme. Three water molecules bind in place of the C alpha- and C beta-hydroxyl and carboxyl groups of isocitrate, while sulfate binds in place of the C gamma-carboxyl group. Side chains of Ser-642 and Arg-447 in the active site rotate to pair with other side chains in the absence of substrate. The new conformation of Arg-447 triggers a concerted set of shifts which transmits conformational change to the surface of the protein, 30 A from the active site. In the absence of substrate, a chain segment containing the [4Fe-4S] ligand Cys-358 also shifts, resulting in the net translation and reorientation of the Fe-S cluster.


    Related Citations: 
    • 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
    • Iron-Sulfur Cluster in Aconitase. Crystallographic Evidence for a Three-Iron Center
      Robbins, A.H.,Stout, C.D.
      (1985) J.Biol.Chem. 260: 2328
    • 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
    • Crystal Structures of Aconitase with Isocitrate and Nitroisocitrate Bound
      Lauble, H.,Kennedy, M.C.,Beinert, H.,Stout, C.D.
      (1992) Biochemistry 31: 2735


    Organizational Affiliation

    Institut für Organische Chemie, Universität Stuttgart, Germany.




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
MIC
Query on MIC

Download SDF File 
Download CCD File 
A
ALPHA-METHYLISOCITRIC ACID
C7 H10 O7
HHKPKXCSHMJWCF-WVBDSBKLSA-N
 Ligand Interaction
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.182 
  • Space Group: B 1 1 2
Unit Cell:
Length (Å)Angle (°)
a = 185.900α = 90.00
b = 71.800β = 90.00
c = 73.200γ = 77.70
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1994-11-11 
  • Released Date: 1995-01-26 
  • Deposition Author(s): Stout, C.D.

Revision History 

  • Version 1.0: 1995-01-26
    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