1CW1

CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE MUTANT K230M BOUND TO ISOCITRATE AND MN2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase.

Cherbavaz, D.B.Lee, M.E.Stroud, R.M.Koshland Jr., D.E.

(2000) J.Mol.Biol. 295: 377-385

  • DOI: 10.1006/jmbi.1999.3195
  • Primary Citation of Related Structures:  1CW4, 1CW7

  • PubMed Abstract: 
  • Isocitrate dehydrogenase catalyses the two step, acid base, oxidative decarboxylation of isocitrate to alpha-ketoglutarate. Lysine 230 was suggested to act as proton donor based on geometry and spatial proximity to isocitrate. To clarify further the ...

    Isocitrate dehydrogenase catalyses the two step, acid base, oxidative decarboxylation of isocitrate to alpha-ketoglutarate. Lysine 230 was suggested to act as proton donor based on geometry and spatial proximity to isocitrate. To clarify further the role of lysine 230, we co-crystallized the lysine-to-methionine mutant (K230M) with isocitrate and with alpha-ketoglutarate. Crystals were flash-frozen and the two structures were determined and refined to 2. 1 A. Several new features were identified relative to the wild-type structure. Seven side-chains previously unplaced in the wild-type structure were identified and included in the model, and the amino acid terminus was extended by an alanine residue. Many additional water molecules were identified. Examination of the K230M active sites (K230M isocitrate and K230M-ketoglutarate) revealed that tyrosine 160 protrudes further into the active site in the presence of either isocitrate or alpha-ketoglutarate in K230 M than it does in the wild-type structure. Also, methionine 230 was not as fully extended, and asparagine 232 rotates approximately 30 degrees toward the ligand permitting polar interactions. Outside the active site cleft a tetragonal volume of density was identified as a sulfate molecule. Its location and interactions suggest it may influence the equilibrium between the tetragonal and the orthorhombic forms of isocitrate dehydrogenase. Differences observed in the active site water structure between the wild-type and K230M structures were due to a single point mutation. A water molecule was located in the position equivalent to that occupied by the wild-type epsilon-amine of lysine 230; a water molecule in that location in K230M suggests it may influence catalysis in the mutant. Comparison of K230M complexed with isocitrate and alpha-ketoglutarate illuminates the influence a ligand has on active site water structure.


    Related Citations: 
    • Catalytic Mechanism of NADP+-dependent Isocitrate Dehydrogenase: Implications from the Structures of Magnesium-isocitrate and NADP+ complexes
      Hurley, J.H.,Dean, A.M.,Koshland Jr., D.E.,Stroud, R.M.
      (1991) Biochemistry 30: 8671
    • Mutational Analysis of the Catalytic Residues Lysine 230 and Tyrosine 160 in the NADP+ Dependent Isocitrate dehydrogenase from Escherichia coli
      Lee, M.E.,Dyer, D.H.,Klein, O.D.,Bolduc, J.M.,Stoddard, B.L.
      (1995) Biochemistry 34: 378


    Organizational Affiliation

    Department of Biochemistry, University of California, San Francisco, San Francisco, CA, 94143-0448, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ISOCITRATE DEHYDROGENASE
A
416Escherichia coli (strain K12)Gene Names: icd (icdA, icdE)
EC: 1.1.1.42
Find proteins for P08200 (Escherichia coli (strain K12))
Go to UniProtKB:  P08200
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ICT
Query on ICT

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.190 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.800α = 90.00
b = 102.800β = 90.00
c = 150.100γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
X-PLORmodel building
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance