4AJS

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate, magnesium(II), Adenosine 2',5'-biphosphate and ribosylnicotinamide-5'-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.802 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase.

Goncalves, S.Miller, S.P.Carrondo, M.A.Dean, A.M.Matias, P.M.

(2012) Biochemistry 51: 7098

  • DOI: 10.1021/bi300483w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NADP(+) dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) belongs to a large family of α-hydroxyacid oxidative β-decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding β-decarboxylat ...

    NADP(+) dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) belongs to a large family of α-hydroxyacid oxidative β-decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding β-decarboxylation to an enol intermediate followed by tautomerization to the final α-ketone product. A comprehensive view of the induced fit needed for catalysis is revealed on comparing the first "fully closed" crystal structures of a pseudo-Michaelis complex of wild-type Escherichia coli IDH (EcoIDH) and the "fully closed" reaction product complex of the K100M mutant with previously obtained "quasi-closed" and "open" conformations. Conserved catalytic residues, binding the nicotinamide ring of NADP(+) and the metal-bound substrate, move as rigid bodies during domain closure by a hinge motion that spans the central β-sheet in each monomer. Interactions established between Thr105 and Ser113, which flank the "phosphorylation loop", and the nicotinamide mononucleotide moiety of NADP(+) establish productive coenzyme binding. Electrostatic interactions of a Lys100-Leu103-Asn115-Glu336 tetrad play a pivotal role in assembling a catalytically competent active site. As predicted, Lys230* is positioned to deprotonate/reprotonate the α-hydroxyl in both reaction steps and Tyr160 moves into position to protonate C3 following β-decarboxylation. A proton relay from the catalytic triad Tyr160-Asp307-Lys230* connects the α-hydroxyl of isocitrate to the bulk solvent to complete the picture of the catalytic mechanism.


    Organizational Affiliation

    Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780 Oeiras Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ISOCITRATE DEHYDROGENASE [NADP]
A
416Escherichia coli (strain K12)Mutation(s): 1 
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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
A2P
Query on A2P

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A
ADENOSINE-2'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
AEOBEOJCBAYXBA-KQYNXXCUSA-N
 Ligand Interaction
ICT
Query on ICT

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A
ISOCITRIC ACID
C6 H8 O7
ODBLHEXUDAPZAU-ZAFYKAAXSA-N
 Ligand Interaction
NMN
Query on NMN

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A
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
NICOTINAMIDE MONONUCLEOTIDE
C11 H16 N2 O8 P
DAYLJWODMCOQEW-TURQNECASA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.802 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.169 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 103.585α = 90.00
b = 103.585β = 90.00
c = 149.680γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release