PDBsum entry: 1fk8

Oxidoreductase

PDB-id

1fk8

	Biological unit* = asymmetric unit, as shown (as deduced by PQS*)


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NAD ×2

Waters ×358

* Residue conservation analysis

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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

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: Q9ZFY9 (Q9ZFY9_COMTE)

Seq:

257 a.a.

Struc:

240 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

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

Related entries:

1fjh
1fjh is the crystal structure of 3-alpha-hydroxysteroid
dehydrogenase from comamonas testosteroni, a member of the
short chain dehydrogenase/reductase family

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Key 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

18175326 A.Yamamura, T.Ichimura, F.Mimoto, J.Ohtsuka, K.Miyazono, M.Okai, M.Kamo, W.C.Lee, K.Nagata, and M.Tanokura (2008).
A unique catalytic triad revealed by the crystal structure of APE0912, a short-chain dehydrogenase/reductase family protein from Aeropyrum pernix K1.

Proteins, 70, 1640-1645.

PDB code: 2z1n

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.

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.

PDB codes: 1nff 1nfq 1nfr

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.

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.