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Oxidoreductase PDB id
1fk8
Jmol
Contents
Protein chains
240 a.a. *
Ligands
NAD ×2
Waters ×358
* Residue conservation analysis
PDB id:
1fk8
Name: Oxidoreductase
Title: The crystal structure of the binary complex with NAD of 3- alpha-hydroxysteroid dehydrogenase from comamonas testosteroni, a member of the short chain dehydrogenase/reductase family
Structure: 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase. Chain: a, b. Synonym: hydroxysteroid short chain dehydrogenase/reductase, 3alpha-hsd/cr. Ec: 1.1.1.50
Source: Comamonas testosteroni. Organism_taxid: 285
Biol. unit: Dimer (from PQS)
Resolution:
1.95Å     R-factor:   0.185     R-free:   0.220
Authors: C.Grimm,R.Ficner,E.Maser,G.Klebe,K.Reuter
Key ref:
C.Grimm et al. (2000). The crystal structure of 3alpha -hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni shows a novel oligomerization pattern within the short chain dehydrogenase/reductase family. J Biol Chem, 275, 41333-41339. PubMed id: 11007791 DOI: 10.1074/jbc.M007559200
Date:
09-Aug-00     Release date:   17-Jan-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P80702  (DIDH_COMTE) -  3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase
Seq:
Struc: 		257 a.a.
240 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.1.1.50  - 3-alpha-hydroxysteroid dehydrogenase (B-specific).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Androsterone + NAD(P)(+) = 5-alpha-androstane-3,17-dione + NAD(P)H
Androsterone
 + NAD(P)(+)
 = 5-alpha-androstane-3,17-dione
 + NAD(P)H
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   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M007559200 J Biol Chem 275:41333-41339 (2000)
PubMed id: 11007791  
 
 
The crystal structure of 3alpha -hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni shows a novel oligomerization pattern within the short chain dehydrogenase/reductase family.
C.Grimm, E.Maser, E.Möbus, G.Klebe, K.Reuter, R.Ficner.
 
  ABSTRACT  
 
The crystal structure of 3alpha-hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni (3alpha-HSDH) as well as the structure of its binary complex with NAD(+) have been solved at 1.68-A and 1.95-A resolution, respectively. The enzyme is a member of the short chain dehydrogenase/reductase (SDR) family. Accordingly, the active center and the conformation of the bound nucleotide cofactor closely resemble those of other SDRs. The crystal structure reveals one homodimer per asymmetric unit representing the physiologically active unity. Dimerization takes place via an interface essentially built-up by helix alphaG and strand betaG of each subunit. So far this type of intermolecular contact has exclusively been observed in homotetrameric SDRs but never in the structure of a homodimeric SDR. The formation of a tetramer is blocked in 3alpha-HSDH by the presence of a predominantly alpha-helical subdomain which is missing in all other SDRs of known structure.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Three-dimensional structure of the 3 -HSDH monomer with bound NAD^+ cosubstrate. The disordered substrate binding loop is indicated by a dotted line. The ribbon representation was produced using the program MOLMOL (33). 		Figure 5.
Fig. 5. Stereo view of residues Asp32 and Ile^33 and the adenosine moiety of the bound NAD^+ cofactor. Asp32, which is highly conserved among NAD(H) preferring SDRs, forms two hydrogen bonds to the 2' and 3' OH group of the adenosine moiety of the bound cofactor. Supposedly, it would form unacceptably short contacts to a potential phosphate group that would be linked to the 2' ogygen in a bound NADP(H) cofactor molecule. The superimposed 2F[obs] F[calc] electron density map is contoured at 1.5 .
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 41333-41339) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21088832 B.Philipp (2011).
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20607749 Y.Zhao, and J.Xiao (2011).
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  J Comput Chem, 32, 33-42.  
20516621 C.Grimm, A.Chari, K.Reuter, and U.Fischer (2010).
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18175326 A.Yamamura, T.Ichimura, F.Mimoto, J.Ohtsuka, K.Miyazono, M.Okai, M.Kamo, W.C.Lee, K.Nagata, and M.Tanokura (2008).
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  Proteins, 70, 1640-1645.
PDB code: 2z1n
19011750 K.L.Kavanagh, H.Jörnvall, B.Persson, and U.Oppermann (2008).
Medium- and short-chain dehydrogenase/reductase gene and protein families : the SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes.
  Cell Mol Life Sci, 65, 3895-3906.  
18566346 R.Zhang, G.Zhu, W.Zhang, S.Cao, X.Ou, X.Li, M.Bartlam, Y.Xu, X.C.Zhang, and Z.Rao (2008).
Crystal structure of a carbonyl reductase from Candida parapsilosis with anti-Prelog stereospecificity.
  Protein Sci, 17, 1412-1423.
PDB code: 3ctm
17958702 K.S.Paithankar, C.Feller, E.B.Kuettner, A.Keim, M.Grunow, and N.Sträter (2007).
Cosubstrate-induced dynamics of D-3-hydroxybutyrate dehydrogenase from Pseudomonas putida.
  FEBS J, 274, 5767-5779.
PDB codes: 2q2q 2q2v 2q2w
  16754984 S.Kataoka, S.Nakamura, T.Ohkubo, S.Ueda, S.Uchiyama, Y.Kobayashi, and M.Oda (2006).
Crystallization and preliminary X-ray analysis of the complex of NADH and 3alpha-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 569-571.  
15906321 A.J.Bordner, and R.Abagyan (2005).
Statistical analysis and prediction of protein-protein interfaces.
  Proteins, 60, 353-366.  
15908576 E.K.Schroeder, L.A.Basso, D.S.Santos, and O.N.de Souza (2005).
Molecular dynamics simulation studies of the wild-type, I21V, and I16T mutants of isoniazid-resistant Mycobacterium tuberculosis enoyl reductase (InhA) in complex with NADH: toward the understanding of NADH-InhA different affinities.
  Biophys J, 89, 876-884.  
16359545 K.Kristan, D.Deluca, J.Adamski, J.Stojan, and T.Lanisnik Rizner (2005).
Dimerization and enzymatic activity of fungal 17beta-hydroxysteroid dehydrogenase from the short-chain dehydrogenase/reductase superfamily.
  BMC Biochem, 6, 28.  
15977159 M.Cohen-Gonsaud, S.Ducasse-Cabanot, A.Quemard, and G.Labesse (2005).
Ligand-induced fit in mycobacterial MabA: the sequence-specific C-terminus locks the conformational change.
  Proteins, 60, 392-400.  
15016358 A.C.Price, Y.M.Zhang, C.O.Rock, and S.W.White (2004).
Cofactor-induced conformational rearrangements establish a catalytically competent active site and a proton relay conduit in FabG.
  Structure, 12, 417-428.
PDB codes: 1q7b 1q7c
15096216 S.Ueda, M.Oda, S.Imamura, and M.Ohnishi (2004).
Transient-phase kinetic studies on the nucleotide binding to 3alpha-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831 using fluorescence stopped-flow procedures.
  Eur J Biochem, 271, 1774-1780.  
12524453 J.K.Yang, M.S.Park, G.S.Waldo, and S.W.Suh (2003).
Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis.
  Proc Natl Acad Sci U S A, 100, 455-460.
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14635134 W.L.Duax, V.Pletnev, A.Addlagatta, J.Bruenn, and C.M.Weeks (2003).
Rational proteomics I. Fingerprint identification and cofactor specificity in the short-chain oxidoreductase (SCOR) enzyme family.
  Proteins, 53, 931-943.  
11841241 E.Maser, B.Völker, and J.Friebertshäuser (2002).
11 Beta-hydroxysteroid dehydrogenase type 1 from human liver: dimerization and enzyme cooperativity support its postulated role as glucocorticoid reductase.
  Biochemistry, 41, 2459-2465.  
12226107 F.Haeseleer, G.F.Jang, Y.Imanishi, C.A.Driessen, M.Matsumura, P.S.Nelson, and K.Palczewski (2002).
Dual-substrate specificity short chain retinol dehydrogenases from the vertebrate retina.
  J Biol Chem, 277, 45537-45546.  
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 code is shown on the right.