1C97 | pdb_00001c97

S642A:ISOCITRATE COMPLEX OF ACONITASE

• PDB DOI: https://doi.org/10.2210/pdb1C97/pdb

• Classification: LYASE
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1999-07-31 Released: 1999-08-12 
• Deposition Author(s): Lloyd, S.J., Lauble, H., Prasad, G.S., Stout, C.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Work: 
  0.218 (Depositor) 
• R-Value Observed: 
  0.218 (Depositor) 

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

• PubMed: 10631981 
• DOI: https://doi.org/10.1110/ps.8.12.2655
• Primary Citation Related Structures: 
  1B0J, 1B0K, 1B0M, 1C96, 1C97


• 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 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.22 kDa 
• Atom Count: 6,429 
• Modeled Residue Count: 753 
• Deposited Residue Count: 753 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MITOCHONDRIAL ACONITASE	A	753	Bos taurus	Mutation(s): 1  EC: 4.2.1.3
UniProt
Find proteins for P20004 (Bos taurus) Explore P20004  Go to UniProtKB:  P20004

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
ICT	D [auth A]	ISOCITRIC ACID C6 H8 O7 ODBLHEXUDAPZAU-ZAFYKAAXSA-N
O	C [auth A]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Work:  0.218 (Depositor) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.4	α = 90
b = 71.4	β = 90
c = 71.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-08-12 
Deposition Author(s): Lloyd, S.J., Lauble, H., Prasad, G.S., Stout, C.D.

Revision History  

• Version 1.0: 1999-08-12
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2018-03-14
  Changes: Database references
• Version 2.0: 2019-02-06
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-02-07
  Changes: Data collection, Database references, Derived calculations