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PDBsum entry 1pb1

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Oxidoreductase PDB id
1pb1
Jmol
Contents
Protein chain
416 a.a. *
Ligands
SO4
ICT
GOL ×3
Waters ×337
* Residue conservation analysis
PDB id:
1pb1
Name: Oxidoreductase
Title: A four location model to explain the stereospecificity of pr
Structure: Isocitrate dehydrogenase [nadp]. Chain: a. Synonym: oxalosuccinate decarboxylase, idh, NADP+-specific engineered: yes. Other_details: wildtype
Source: Escherichia coli. Organism_taxid: 562. Gene: icd or icda or icde or b1136. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
1.70Å     R-factor:   0.185     R-free:   0.211
Authors: A.D.Mesecar,D.E.Koshland Jr.
Key ref: A.D.Mesecar and D.E.Koshland (2000). A new model for protein stereospecificity. Nature, 403, 614-615. PubMed id: 10688187 DOI: 10.1038/35001144
Date:
14-May-03     Release date:   17-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08200  (IDH_ECOLI) -  Isocitrate dehydrogenase [NADP]
Seq:
Struc:
416 a.a.
416 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     cytoplasm   1 term 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1038/35001144 Nature 403:614-615 (2000)
PubMed id: 10688187  
 
 
A new model for protein stereospecificity.
A.D.Mesecar, D.E.Koshland.
 
  ABSTRACT  
 
No abstract given.

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19680237 D.Foschini, R.C.Araújo, R.F.Bacurau, A.De Piano, S.S.De Almeida, J.Carnier, T.D.Rosa, M.T.De Mello, S.Tufik, and A.R.Dâmaso (2010).
Treatment of obese adolescents: the influence of periodization models and ACE genotype.
  Obesity (Silver Spring), 18, 766-772.  
20734058 G.Rodríguez-Romo, J.R.Ruiz, C.Santiago, C.Fiuza-Luces, M.González-Freire, F.Gómez-Gallego, M.Morán, and A.Lucia (2010).
Does the ACE I/D polymorphism, alone or in combination with the ACTN3 R577X polymorphism, influence muscle power phenotypes in young, non-athletic adults?
  Eur J Appl Physiol, 110, 1099-1106.  
20957098 P.S.Dieng, and C.Sirlin (2010).
Recognition of chiral carboxylic anions by artificial receptors.
  Int J Mol Sci, 11, 3334-3348.  
19458960 A.M.Costa, A.J.Silva, N.D.Garrido, H.Louro, R.J.de Oliveira, and L.Breitenfeld (2009).
Association between ACE D allele and elite short distance swimming.
  Eur J Appl Physiol, 106, 785-790.  
19103212 D.F.Covey (2009).
ent-Steroids: novel tools for studies of signaling pathways.
  Steroids, 74, 577-585.  
19472280 D.I.Ranieri, H.Hofstetter, and O.Hofstetter (2009).
Computational structural analysis of an anti-L-amino acid antibody and inversion of its stereoselectivity.
  J Sep Sci, 32, 1686-1695.  
19672908 J.H.Park, H.J.Ha, W.K.Lee, T.Généreux-Vincent, and R.J.Kazlauskas (2009).
Molecular basis for the stereoselective ammoniolysis of N-alkyl aziridine-2-carboxylates catalyzed by Candida antarctica lipase B.
  Chembiochem, 10, 2213-2222.  
19935855 S.K.Min, K.Takahashi, H.Ishigami, K.Hiranuma, M.Mizuno, T.Ishii, C.S.Kim, and K.Nakazato (2009).
Is there a gender difference between ACE gene and race distance?
  Appl Physiol Nutr Metab, 34, 926-932.  
18172831 D.I.Ranieri, D.M.Corgliano, E.J.Franco, H.Hofstetter, and O.Hofstetter (2008).
Investigation of the stereoselectivity of an anti-amino acid antibody using molecular modeling and ligand docking.
  Chirality, 20, 559-570.  
18723411 K.Jozwiak, R.Moaddel, S.Ravichandran, A.Plazinska, J.Kozak, S.Patel, R.Yamaguchi, and I.W.Wainer (2008).
Exploring enantiospecific ligand-protein interactions using cellular membrane affinity chromatography: chiral recognition as a dynamic process.
  J Chromatogr B Analyt Technol Biomed Life Sci, 875, 200-207.  
18852458 K.Ratia, S.Pegan, J.Takayama, K.Sleeman, M.Coughlin, S.Baliji, R.Chaudhuri, W.Fu, B.S.Prabhakar, M.E.Johnson, S.C.Baker, A.K.Ghosh, and A.D.Mesecar (2008).
A noncovalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication.
  Proc Natl Acad Sci U S A, 105, 16119-16124.  
18221369 Z.Buraei, and K.S.Elmslie (2008).
The separation of antagonist from agonist effects of trisubstituted purines on CaV2.2 (N-type) channels.
  J Neurochem, 105, 1450-1461.  
18217598 K.Aburaya, I.Hisaki, N.Tohnai, and M.Miyata (2007).
Dependence of the enantioselectivity on reversion of layer directions in cholamide inclusion compounds.
  Chem Commun (Camb), (), 4257-4259.  
17610893 M.May, S.Mehboob, D.C.Mulhearn, Z.Wang, H.Yu, G.R.Thatcher, B.D.Santarsiero, M.E.Johnson, and A.D.Mesecar (2007).
Structural and functional analysis of two glutamate racemase isozymes from Bacillus anthracis and implications for inhibitor design.
  J Mol Biol, 371, 1219-1237.
PDB codes: 2dwu 2gzm
17006713 H.Wagner, S.Thaller, R.Dahse, and M.Sust (2006).
Biomechanical muscle properties and angiotensin-converting enzyme gene polymorphism: a model-based study.
  Eur J Appl Physiol, 98, 507-515.  
16528762 R.Wombacher, S.Keiper, S.Suhm, A.Serganov, D.J.Patel, and A.Jäschke (2006).
Control of stereoselectivity in an enzymatic reaction by backdoor access.
  Angew Chem Int Ed Engl, 45, 2469-2472.  
15726413 D.G.Macarthur, and K.N.North (2005).
Genes and human elite athletic performance.
  Hum Genet, 116, 331-339.  
15736174 V.Sundaresan, and R.Abrol (2005).
Biological chiral recognition: the substrate's perspective.
  Chirality, 17, S30-S39.  
15702370 E.J.Westover, and D.F.Covey (2004).
The enantiomer of cholesterol.
  J Membr Biol, 202, 61-72.  
12467043 K.Kato, Y.Aoki, M.Sugahara, N.Tohnai, K.Sada, and M.Miyata (2003).
Interpretation of enantioresolution in nordeoxycholic acid channels based on the four-location model.
  Chirality, 15, 53-59.  
12021432 V.Sundaresan, and R.Abrol (2002).
Towards a general model for protein-substrate stereoselectivity.
  Protein Sci, 11, 1330-1339.  
10841540 B.P.Klaholz, A.Mitschler, M.Belema, C.Zusi, and D.Moras (2000).
Enantiomer discrimination illustrated by high-resolution crystal structures of the human nuclear receptor hRARgamma.
  Proc Natl Acad Sci U S A, 97, 6322-6327.
PDB codes: 1exa 1exx
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.