1B0J

CRYSTAL STRUCTURE OF ACONITASE WITH ISOCITRATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report



Literature

The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex

Lloyd, S.J.Lauble, H.Prasad, G.S.Stout, C.D.

(1999) Protein Sci 8: 2655-2662

  • DOI: 10.1110/ps.8.12.2655
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of the S642A mutant of mitochondrial aconitase (mAc) with citrate bound has been determined at 1.8 A resolution and 100 K to capture this binding mode of substrates to the native enzyme. The 2.0 A resolution, 100 K crystal struc ...

    The crystal structure of the S642A mutant of mitochondrial aconitase (mAc) with citrate bound has been determined at 1.8 A resolution and 100 K to capture this binding mode of substrates to the native enzyme. The 2.0 A resolution, 100 K crystal structure of the S642A mutant with isocitrate binding provides a control, showing that the Ser --> Ala replacement does not alter the binding of substrates in the active site. The aconitase mechanism requires that the intermediate product, cis-aconitate, flip over by 180 degrees about the C alpha-C beta double bond. Only one of these two alternative modes of binding, that of the isocitrate mode, has been previously visualized. Now, however, the structure revealing the citrate mode of binding provides direct support for the proposed enzyme mechanism.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACONITATE HYDRATASE
A
754Sus scrofaMutation(s): 1 
Gene Names: ACO2
EC: 4.2.1.3
Find proteins for P16276 (Sus scrofa)
Go to UniProtKB:  P16276
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

Download CCD File 
A
ISOCITRIC ACID
C6 H8 O7
ODBLHEXUDAPZAU-ZAFYKAAXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.162 
  • R-Value Observed: 0.162 
  • Space Group: B 1 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.4α = 90
b = 72.1β = 90
c = 73.9γ = 77.7
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data reduction
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 2.0: 2019-02-06
    Changes: Advisory, Atomic model, Data collection, Derived calculations