The crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogenase from Rhodococcus jostii RHA1

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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Structure and Catalytic Mechanism of 3-Ketosteroid-{Delta}4-(5Alpha)-Dehydrogenase from Rhodococcus Jostii Rha1 Genome.

Van Oosterwijk, N.Knol, J.Dijkhuizen, L.Van Der Geize, R.Dijkstra, B.W.

(2012) J Biol Chem 287: 30975

  • DOI: https://doi.org/10.1074/jbc.M112.374306
  • Primary Citation of Related Structures:  
    4AT0, 4AT2

  • PubMed Abstract: 

    3-Ketosteroid Δ4-(5α)-dehydrogenases (Δ4-(5α)-KSTDs) are enzymes that introduce a double bond between the C4 and C5 atoms of 3-keto-(5α)-steroids. Here we show that the ro05698 gene from Rhodococcus jostii RHA1 codes for a flavoprotein with Δ4-(5α)-KSTD activity. The 1.6 Å resolution crystal structure of the enzyme revealed three conserved residues (Tyr-319, Tyr-466, and Ser-468) in a pocket near the isoalloxazine ring system of the FAD co-factor. Site-directed mutagenesis of these residues confirmed that they are absolutely essential for catalytic activity. A crystal structure with bound product 4-androstene-3,17-dione showed that Ser-468 is in a position in which it can serve as the base abstracting the 4β-proton from the C4 atom of the substrate. Ser-468 is assisted by Tyr-319, which possibly is involved in shuttling the proton to the solvent. Tyr-466 is at hydrogen bonding distance to the C3 oxygen atom of the substrate and can stabilize the keto-enol intermediate occurring during the reaction. Finally, the FAD N5 atom is in a position to be able to abstract the 5α-hydrogen of the substrate as a hydride ion. These features fully explain the reaction catalyzed by Δ4-(5α)-KSTDs.

  • Organizational Affiliation

    Laboratory of Biophysical Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE510Rhodococcus jostii RHA1Mutation(s): 0 
Gene Names: RHA1_ro05698
Find proteins for Q0S4Q9 (Rhodococcus jostii (strain RHA1))
Explore Q0S4Q9 
Go to UniProtKB:  Q0S4Q9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0S4Q9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.233α = 90
b = 114.308β = 90
c = 110.161γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2012-10-10
    Changes: Database references