Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 83229.65 
• Atom Count: 5826 
• Residue Count: 754 
• Unique protein chains: 1

1AMJ

STERIC AND CONFORMATIONAL FEATURES OF THE ACONITASE MECHANISM

• DOI: 10.2210/pdb1AMJ/pdb

• Classification: LYASE(CARBON-OXYGEN)
• Organism(s): Bos taurus


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.168 

Literature

Steric and conformational features of the aconitase mechanism.

Lauble, H., Stout, C.D.

(1995) Proteins 22: 1-11

• PubMed: 7675781 
• DOI: 10.1002/prot.340220102
• Primary Citation of Related Structures:  
  1AMI


• 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 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.

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Related Citations: 

• The Structure of Aconitase
  Robbins, A.H.,Stout, C.D.
  (1989) Proteins 5: 289
• Crystal Structures of Aconitase with Isocitrate and Nitroisocitrate Bound
  Lauble, H.,Kennedy, M.C.,Beinert, H.,Stout, C.D.
  (1992) Biochemistry 31: 2735
• 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 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




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Organizational Affiliation: 

Institut für Organische Chemie, Universität Stuttgart, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ACONITASE	A	754	Bos taurus	Mutation(s): 0  Gene 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SF4	A	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
OH	A	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.168 
• Space Group: B 1 1 2

Unit Cell:

Length (Å)	Angle (°)
a = 185.500	α = 90.00
b = 72.000	β = 90.00
c = 73.000	γ = 77.70

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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