3COT

Crystal structure of human liver delta(4)-3-ketosteroid 5beta-reductase (akr1d1) in complex with progesterone and nadp. Resolution: 2.03 A.

Summary for 3COT

• Entry DOI: 10.2210/pdb3cot/pdb
• Related: 3CMF
• Descriptor: 3-oxo-5-beta-steroid 4-dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, PROGESTERONE, ... (4 entities in total)
• Functional Keywords: steroid c-c double bond reduction, 5beta reductase, e120, bile acid catabolism, cytoplasm, disease mutation, lipid metabolism, nadp, oxidoreductase, steroid metabolism
• Biological source: Homo sapiens (human)
• Cellular location: Cytoplasm: P51857
• Total number of polymer chains: 2
• Total formula weight: 81314.25

Authors

Di Costanzo, L.,Drury, J.,Penning, T.M.,Christianson, D.W. (deposition date: 2008-03-29, release date: 2008-04-08, Last modification date: 2023-08-30)

Primary citation

Di Costanzo, L.,Drury, J.E.,Penning, T.M.,Christianson, D.W.
Crystal Structure of Human Liver {Delta}4-3-Ketosteroid 5{beta}-Reductase (AKR1D1) and Implications for Substrate Binding and Catalysis.
J.Biol.Chem., 283:16830-16839, 2008

PubMed Abstract: AKR1D1 (steroid 5beta-reductase) reduces all Delta(4)-3-ketosteroids to form 5beta-dihydrosteroids, a first step in the clearance of steroid hormones and an essential step in the synthesis of all bile acids. The reduction of the carbon-carbon double bond in an alpha,beta-unsaturated ketone by 5beta-reductase is a unique reaction in steroid enzymology because hydride transfer from NADPH to the beta-face of a Delta(4)-3-ketosteroid yields a cis-A/B-ring configuration with an approximately 90 degrees bend in steroid structure. Here, we report the first x-ray crystal structure of a mammalian steroid hormone carbon-carbon double bond reductase, human Delta(4)-3-ketosteroid 5beta-reductase (AKR1D1), and its complexes with intact substrates. We have determined the structures of AKR1D1 complexes with NADP(+) at 1.79- and 1.35-A resolution (HEPES bound in the active site), NADP(+) and cortisone at 1.90-A resolution, NADP(+) and progesterone at 2.03-A resolution, and NADP(+) and testosterone at 1.62-A resolution. Complexes with cortisone and progesterone reveal productive substrate binding orientations based on the proximity of each steroid carbon-carbon double bond to the re-face of the nicotinamide ring of NADP(+). This orientation would permit 4-pro-(R)-hydride transfer from NADPH. Each steroid carbonyl accepts hydrogen bonds from catalytic residues Tyr(58) and Glu(120). The Y58F and E120A mutants are devoid of activity, supporting a role for this dyad in the catalytic mechanism. Intriguingly, testosterone binds nonproductively, thereby rationalizing the substrate inhibition observed with this particular steroid. The locations of disease-linked mutations thought to be responsible for bile acid deficiency are also revealed.

PubMed: 18407998
DOI: 10.1074/jbc.M801778200

Experimental method

X-RAY DIFFRACTION (2.03 Å)