PDBsum entry 3map

Oxidoreductase

PDB id: 3map

Contents

Protein chain

397 a.a. *

Ligands

NAP ×2

ICT ×2

* Residue conservation analysis

PDB id:

3map

Name:

Oxidoreductase

Title:

Crystal structure of homodimeric r132h mutant of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP and isocitrate

Structure:

Isocitrate dehydrogenase [nadp] cytoplasmic. Chain: a, b. Synonym: idh, cytosolic NADP-isocitrate dehydrogenase, oxalosuccinate decarboxylase, NADP(+)-specific icdh, idp. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: idh1, picd. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.227 R-free: 0.269

Authors:

B.Yang,Y.Peng,J.Ding

Key ref:

B.Yang et al. (2010). Molecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H. Cell Res, 20, 1188-1200. PubMed id: 20975740

Date:

24-Mar-10 Release date: 10-Nov-10

Protein chains

O75874  (IDHC_HUMAN) -  Isocitrate dehydrogenase [NADP] cytoplasmic from Homo sapiens

Seq: 414 a.a.

Struc: 397 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.1.1.42 - isocitrate dehydrogenase (NADP(+)).
• Pathway: Citric acid cycle
• Reaction: D-threo-isocitrate + NADP⁺ = 2-oxoglutarate + CO2 + NADPH

D-threo-isocitrate + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = 2-oxoglutarate (Bound ligand (Het Group name = ICT) matches with 76.92% similarity) + CO2 + NADPH

• Cofactor: Mn(2+) or Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Cell Res 20:1188-1200 (2010)

PubMed id: 20975740

Molecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H.

B.Yang, C.Zhong, Y.Peng, Z.Lai, J.Ding.

ABSTRACT

Human cytosolic NADP-IDH (IDH1) has recently been found to be involved in tumorigenesis. Notably, the tumor-derived IDH1 mutations identified so far mainly occur at Arg132, and mutation R132H is the most prevalent one. This mutation impairs the oxidative IDH activity of the enzyme, but renders a new reduction function of converting α-ketoglutarate (αKG) to 2-hydroxyglutarate. Here, we report the structures of the R132H mutant IDH1 with and without isocitrate (ICT) bound. The structural data together with mutagenesis and biochemical data reveal a previously undefined initial ICT-binding state and demonstrate that IDH activity requires a conformational change to a closed pre-transition state. Arg132 plays multiple functional roles in the catalytic reaction; in particular, the R132H mutation hinders the conformational changes from the initial ICT-binding state to the pre-transition state, leading to the impairment of the IDH activity. Our results describe for the first time that there is an intermediate conformation that corresponds to an initial ICT-binding state and that the R132H mutation can trap the enzyme in this conformation, therefore shedding light on the molecular mechanism of the "off switch" of the potentially tumor-suppressive IDH activity. Furthermore, we proved the necessity of Tyr139 for the gained αKG reduction activity and propose that Tyr139 may play a vital role by compensating the increased negative charge on the C2 atom of αKG during the transfer of a hydride anion from NADPH to αKG, which provides new insights into the mechanism of the "on switch" of the hypothetically oncogenic reduction activity of IDH1 by this mutation.