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PDBsum entry 1lwd

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1lwd
Jmol
Contents
Protein chains
413 a.a. *
Ligands
ICT ×2
SO4 ×2
Metals
_MN ×2
Waters ×715
* Residue conservation analysis
PDB id:
1lwd
Name: Oxidoreductase
Title: Crystal structure of NADP-dependent isocitrate dehydrogenase from porcine heart mitochondria
Structure: Isocitrate dehydrogenase. Chain: a, b. Synonym: oxalosuccinate decarboxylase, idh, NADP+-specific icdh, idp, icd-m. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organ: heart. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.85Å     R-factor:   0.182     R-free:   0.210
Authors: C.Ceccarelli,B.J.Bahnson
Key ref:
C.Ceccarelli et al. (2002). Crystal structure of porcine mitochondrial NADP+-dependent isocitrate dehydrogenase complexed with Mn2+ and isocitrate. Insights into the enzyme mechanism. J Biol Chem, 277, 43454-43462. PubMed id: 12207025 DOI: 10.1074/jbc.M207306200
Date:
31-May-02     Release date:   13-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P33198  (IDHP_PIG) -  Isocitrate dehydrogenase [NADP], mitochondrial (Fragment)
Seq:
Struc:
421 a.a.
413 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.42  - Isocitrate dehydrogenase (NADP(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Citric acid cycle
      Reaction: Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH
Isocitrate
Bound ligand (Het Group name = ICT)
corresponds exactly
+ NADP(+)
= 2-oxoglutarate
+ CO(2)
+ NADPH
      Cofactor: Mn(2+) or Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   2 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M207306200 J Biol Chem 277:43454-43462 (2002)
PubMed id: 12207025  
 
 
Crystal structure of porcine mitochondrial NADP+-dependent isocitrate dehydrogenase complexed with Mn2+ and isocitrate. Insights into the enzyme mechanism.
C.Ceccarelli, N.B.Grodsky, N.Ariyaratne, R.F.Colman, B.J.Bahnson.
 
  ABSTRACT  
 
The crystal structure of porcine heart mitochondrial NADP+-dependent isocitrate dehydrogenase (IDH) complexed with Mn2+ and isocitrate was solved to a resolution of 1.85 A. The enzyme was expressed in Escherichia coli, purified as a fusion protein with maltose binding protein, and cleaved with thrombin to yield homogeneous enzyme. The structure was determined by multiwavelength anomalous diffraction phasing using selenium substitution in the form of selenomethionine as the anomalous scatterer. The porcine NADP+-IDH enzyme is structurally compared with the previously solved structures of IDH from E. coli and Bacillus subtilis that share 16 and 17% identity, respectively, with the mammalian enzyme. The porcine enzyme has a protein fold similar to the bacterial IDH structures with each monomer folding into two domains. However, considerable differences exist between the bacterial and mammalian forms of IDH in regions connecting core secondary structure. Based on the alignment of sequence and structure among the porcine, E. coli, and B. subtilis IDH, a putative phosphorylation site has been identified for the mammalian enzyme. The active site, including the bound Mn2+-isocitrate complex, is highly ordered and, therefore, mechanistically informative. The consensus IDH mechanism predicts that the Mn2+-bound hydroxyl of isocitrate is deprotonated prior to its NADP+-dependent oxidation. The present crystal structure has an active site water that is well positioned to accept the proton and ultimately transfer the proton to solvent through an additional bound water.
 
  Selected figure(s)  
 
Figure 6.
Fig. 6. Active site waters in the Mn2+-isocitrate porcine IDH complex. The active site Mn2+-isocitrate complex is shown from subunit B with the two active site water molecules w6 and w8 hydrogen bonding with Asp252 and Asp253. The Mn2+ ligand Asp275, which occupies the axial ligand position behind the Mn2+, is not shown in this view.
Figure 7.
Fig. 7. Mechanism of the NADP+-dependent oxidation of IDH. The first step illustrates how an ordered active site water (w6) from the porcine IDH structure accepts the proton from the Mn2+-bound isocitrate hydroxyl. This bound water is within hydrogen bonding distance of a second bound water (w8). The remote bound water w8 is solvent accessible on the surface of IDH. The measured pK[a] of 5.6 from pH versus V[max] rate profiles is likely to directly indicate the pK[a] for the Mn2+-coordinated hydroxyl proton.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 43454-43462) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20615753 N.K.Kloosterhof, L.B.Bralten, H.J.Dubbink, P.J.French, and M.J.van den Bent (2011).
Isocitrate dehydrogenase-1 mutations: a fundamentally new understanding of diffuse glioma?
  Lancet Oncol, 12, 83-91.  
20975740 B.Yang, C.Zhong, Y.Peng, Z.Lai, and J.Ding (2010).
Molecular mechanisms of "off-on switch" of activities of human IDH1 by tumor-associated mutation R132H.
  Cell Res, 20, 1188-1200.
PDB codes: 3map 3mar 3mas
20972461 K.E.Yen, M.A.Bittinger, S.M.Su, and V.R.Fantin (2010).
Cancer-associated IDH mutations: biomarker and therapeutic opportunities.
  Oncogene, 29, 6409-6417.  
20171147 P.S.Ward, J.Patel, D.R.Wise, O.Abdel-Wahab, B.D.Bennett, H.A.Coller, J.R.Cross, V.R.Fantin, C.V.Hedvat, A.E.Perl, J.D.Rabinowitz, M.Carroll, S.M.Su, K.A.Sharp, R.L.Levine, and C.B.Thompson (2010).
The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate.
  Cancer Cell, 17, 225-234.  
20516620 R.Malik, and R.E.Viola (2010).
Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions.
  Acta Crystallogr D Biol Crystallogr, 66, 673-684.
PDB codes: 3flk 3fmx
20513808 Z.J.Reitman, and H.Yan (2010).
Isocitrate dehydrogenase 1 and 2 mutations in cancer: alterations at a crossroads of cellular metabolism.
  J Natl Cancer Inst, 102, 932-941.  
19530703 Y.Lin, A.H.West, and P.F.Cook (2009).
Site-directed mutagenesis as a probe of the acid-base catalytic mechanism of homoisocitrate dehydrogenase from Saccharomyces cerevisiae.
  Biochemistry, 48, 7305-7312.  
18256028 A.B.Taylor, G.Hu, P.J.Hart, and L.McAlister-Henn (2008).
Allosteric motions in structures of yeast NAD+-specific isocitrate dehydrogenase.
  J Biol Chem, 283, 10872-10880.
PDB codes: 3blv 3blw 3blx
18275837 Q.Lu, K.I.Minard, and L.McAlister-Henn (2008).
Dual compartmental localization and function of mammalian NADP+-specific isocitrate dehydrogenase in yeast.
  Arch Biochem Biophys, 472, 17-25.  
18552125 Y.Peng, C.Zhong, W.Huang, and J.Ding (2008).
Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction.
  Protein Sci, 17, 1542-1554.
PDB codes: 2qfv 2qfw 2qfx 2qfy
17160675 R.Stokke, D.Madern, A.E.Fedøy, S.Karlsen, N.K.Birkeland, and I.H.Steen (2007).
Biochemical characterization of isocitrate dehydrogenase from Methylococcus capsulatus reveals a unique NAD+-dependent homotetrameric enzyme.
  Arch Microbiol, 187, 361-370.  
17401542 R.Stokke, M.Karlström, N.Yang, I.Leiros, R.Ladenstein, N.K.Birkeland, and I.H.Steen (2007).
Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers.
  Extremophiles, 11, 481-493.
PDB code: 2iv0
17123127 R.Stokke, N.K.Birkeland, and I.H.Steen (2007).
Thermal stability and biochemical properties of isocitrate dehydrogenase from the thermoacidophilic archaeon Thermoplasma acidophilum.
  Extremophiles, 11, 397-402.  
16759231 M.Karlström, I.H.Steen, D.Madern, A.E.Fedöy, N.K.Birkeland, and R.Ladenstein (2006).
The crystal structure of a hyperthermostable subfamily II isocitrate dehydrogenase from Thermotoga maritima.
  FEBS J, 273, 2851-2868.
PDB code: 1zor
16767773 O.V.Kalinina, and M.S.Gelfand (2006).
Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenases.
  Proteins, 64, 1001-1009.  
16889632 S.C.Chang, K.Y.Lin, Y.J.Chen, C.H.Lai, G.G.Chang, and W.Y.Chou (2006).
Critical roles of conserved carboxylic acid residues in pigeon cytosolic NADP+-dependent malic enzyme.
  FEBS J, 273, 4072-4081.  
15576556 T.K.Kim, and R.F.Colman (2005).
Ser95, Asn97, and Thr78 are important for the catalytic function of porcine NADP-dependent isocitrate dehydrogenase.
  Protein Sci, 14, 140-147.  
15062079 P.P.Iyer, S.H.Lawrence, K.B.Luther, K.R.Rajashankar, H.P.Yennawar, J.G.Ferry, and H.Schindelin (2004).
Crystal structure of phosphotransacetylase from the methanogenic archaeon Methanosarcina thermophila.
  Structure, 12, 559-567.
PDB code: 1qzt
12694190 C.Wrenger, and S.Müller (2003).
Isocitrate dehydrogenase of Plasmodium falciparum.
  Eur J Biochem, 270, 1775-1783.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.