4AT2

The crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogenase from Rhodococcus jostii RHA1 in complex with 4-androstene-3,17- dione

Summary for 4AT2

• Entry DOI: 10.2210/pdb4at2/pdb
• Related: 4AT0
• Descriptor: 3-KETOSTEROID-DELTA4-5ALPHA-DEHYDROGENASE, 4-ANDROSTENE-3-17-DIONE, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: oxidoreductase, steroid catabolism
• Biological source: RHODOCOCCUS JOSTII
• Total number of polymer chains: 1
• Total formula weight: 55191.01

Authors

van Oosterwijk, N.,Knol, J.,Dijkhuizen, L.,van der Geize, R.,Dijkstra, B.W. (deposition date: 2012-05-03, release date: 2012-08-01, Last modification date: 2024-05-08)

Primary citation

Van Oosterwijk, N.,Knol, J.,Dijkhuizen, L.,Van Der Geize, R.,Dijkstra, B.W.
Structure and Catalytic Mechanism of 3-Ketosteroid-{Delta}4-(5Alpha)-Dehydrogenase from Rhodococcus Jostii Rha1 Genome.
J.Biol.Chem., 287:30975-, 2012

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.

PubMed: 22833669
DOI: 10.1074/JBC.M112.374306

Experimental method

X-RAY DIFFRACTION (1.6 Å)