PDBsum entry 1cw1

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Oxidoreductase PDB id
Protein chain
415 a.a. *
Waters ×332
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of isocitrate dehydrogenase mutant k230m b isocitrate and mn2+
Structure: Isocitrate dehydrogenase. Chain: a. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
2.10Å     R-factor:   0.190     R-free:   0.233
Authors: R.Stroud,J.Finer-Moore
Key ref:
D.B.Cherbavaz et al. (2000). Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase. J Mol Biol, 295, 377-385. PubMed id: 10623532 DOI: 10.1006/jmbi.1999.3195
25-Aug-99     Release date:   01-Sep-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P08200  (IDH_ECOLI) -  Isocitrate dehydrogenase [NADP]
416 a.a.
415 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

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

Citric acid cycle
      Reaction: Isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH
Bound ligand (Het Group name = ICT)
corresponds exactly
+ NADP(+)
= 2-oxoglutarate
+ CO(2)
      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     cytoplasm   1 term 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     6 terms  


DOI no: 10.1006/jmbi.1999.3195 J Mol Biol 295:377-385 (2000)
PubMed id: 10623532  
Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase.
D.B.Cherbavaz, M.E.Lee, R.M.Stroud, D.E.Koshland.
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.
  Selected figure(s)  
Figure 1.
Figure 1. Superposed active site residues from three low temperature structures of isocitrate dehydrogenase illustrates the relative position of designated matched water molecules. Numbers 1 through 13 correspond to water molecules described in Table 2A. Active site residues are labeled with amino acid type and sequence number except for 230, which is lysine in wild-type and methionine in K230M. The red, orange, and yellow residues and water molecules represent wild-type-isocitrate, K230M-isocitrate, and K230M-a-ketoglutarate structures, respectively. (a) Illustration of all active site water molecules outlined in Table 2 and their position relative to active site residues. Water 11 occupies a position in the K230M structures similar to the position the epsilon -anime hydrogen atoms of K230 occupy in the wild-type structure. Water molecules 8, 9, and 11 specifically appear in the K230M mutant structures. (b) Positional differences in the hydroxyl oxygen atom of tyrosine 160 are highlighted in this view. The two views are related by rotation of approximately 50 °.
Figure 2.
Figure 2. Molecular surface of IDH shown with ligands bound. (a) Isocitrate is presented in the cavernous active site pocket. (b) NADP and isocitrate are shown in the extended active site volume. The adenine moiety of NADP+ (top) is bound in a narrow pocket contiguous with the isocitrate active site. The nicotinamide moiety of NADP+ associates with isocitrate and occupies part of the dehydrogenase active site. The sulfate molecule located in the K230M structures is visible, below and exterior to the active site pocket (present in both (a) and (b)). The NADP+ coordinates were supplied by PDB files reported by [Stoddard et al 1993]. The molecular contours corresponding to Van der Waals surfaces were prepared using Grasp [Sridharan et al 1995].
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 295, 377-385) copyright 2000.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21469159 S.Y.Lu, Y.J.Jiang, J.Lv, J.W.Zou, and T.X.Wu (2011).
Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies.
  J Comput Chem, 32, 1907-1918.  
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
18366016 D.Katagiri, H.Fuji, S.Neya, and T.Hoshino (2008).
Ab initio protein structure prediction with force field parameters derived from water-phase quantum chemical calculation.
  J Comput Chem, 29, 1930-1944.  
16374623 A.T.García-Sosa, and R.L.Mancera (2006).
The effect of a tightly bound water molecule on scaffold diversity in the computer-aided de novo ligand design of CDK2 inhibitors.
  J Mol Model, 12, 422-431.  
16284723 A.Rodríguez-Arnedo, M.Camacho, F.Llorca, and M.J.Bonete (2005).
Complete reversal of coenzyme specificity of isocitrate dehydrogenase from Haloferax volcanii.
  Protein J, 24, 259-266.  
12756610 A.T.García-Sosa, R.L.Mancera, and P.M.Dean (2003).
WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.
  J Mol Model, 9, 172-182.  
14512428 T.K.Kim, P.Lee, and R.F.Colman (2003).
Critical role of Lys212 and Tyr140 in porcine NADP-dependent isocitrate dehydrogenase.
  J Biol Chem, 278, 49323-49331.  
12855708 Y.Yasutake, S.Watanabe, M.Yao, Y.Takada, N.Fukunaga, and I.Tanaka (2003).
Crystal structure of the monomeric isocitrate dehydrogenase in the presence of NADP+: insight into the cofactor recognition, catalysis, and evolution.
  J Biol Chem, 278, 36897-36904.
PDB code: 1j1w
12207025 C.Ceccarelli, N.B.Grodsky, N.Ariyaratne, R.F.Colman, and B.J.Bahnson (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.
PDB code: 1lwd
12007799 M.Camacho, A.Rodríguez-Arnedo, and M.J.Bonete (2002).
NADP-dependent isocitrate dehydrogenase from the halophilic archaeon Haloferax volcanii: cloning, sequence determination and overexpression in Escherichia coli.
  FEMS Microbiol Lett, 209, 155-160.  
11751849 S.K.Singh, S.P.Miller, A.Dean, L.J.Banaszak, and D.C.LaPorte (2002).
Bacillus subtilis isocitrate dehydrogenase. A substrate analogue for Escherichia coli isocitrate dehydrogenase kinase/phosphatase.
  J Biol Chem, 277, 7567-7573.  
11679744 Y.Yasutake, S.Watanabe, M.Yao, Y.Takada, N.Fukunaga, and I.Tanaka (2001).
Crystallization and preliminary X-ray diffraction studies of monomeric isocitrate dehydrogenase by the MAD method using Mn atoms.
  Acta Crystallogr D Biol Crystallogr, 57, 1682-1685.  
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.