1LWI image
Deposition Date 1996-02-24
Release Date 1996-12-07
Last Version Date 2024-02-14
Entry Detail
PDB ID:
1LWI
Keywords:
Title:
3-ALPHA-HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE FROM RATTUS NORVEGICUS
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.70 Å
R-Value Free:
0.29
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:3-ALPHA-HYDROXYSTEROID/DIHYDRODIOL DEHYDROGENASE
Gene (Uniprot):Akr1c9
Chain IDs:A, B
Chain Length:322
Number of Molecules:2
Biological Source:Rattus norvegicus
Ligand Molecules
Primary Citation
Structure of 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase complexed with NADP+.
Biochemistry 35 10702 10711 (1996)
PMID: 8718859 DOI: 10.1021/bi9604688

Abstact

Rat liver 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase (3 alpha-HSD) inactivates circulating steroid hormones and is involved in polycyclic aromatic hydrocarbon (PAH) carcinogenesis. It is the only HSD of known structure in the aldo-keto reductase (AKR) superfamily and may provide a paradigm for other mammalian HSDs in this family. The structure of the 3 alpha-HSD.NADP+ binary complex has been determined at 2.7 A resolution and refined to a crystallographic R-factor of 23.4% with good geometry. The model is similar to other binary complexes in the AKR superfamily in that NADP+ binds at the C-terminal end of an alpha/beta barrel. However, it is unique in that NADP+ is bound in two alternate conformations, probably because of the lack of a salt-linked "safety belt" over the pyrophosphate bridge. The structure supports a previously proposed catalytic mechanism for carbonyl reduction in which Tyr 55 is the general acid, and its effective pKa is lowered by the adjacent Lys 84. We present evidence that the structurally distinct short-chain dehydrogenase/reductase (SDR) superfamily may have convergently evolved a similar catalytic mechanism. Insight into substrate binding is offered by a crystal packing contact in which a neighboring molecule inserts a tryptophan residue (Trp 227) into an apolar cleft in 3 alpha-HSD. This cleft is proximal to the bound NADP+ cofactor and contains a surface of apolar residues (Leu 54, Trp 86, Leu 122, Phe 128, Phe 129, Leu 137, Phe 139), making it a likely candidate for the substrate-binding site. Thus, in forming this crystal contact, Trp 227 may mimic a portion of a bound steroid. In addition, we propose that a water molecule in the active site indicates the position of the hydroxyl oxygen in a 3 alpha-hydroxysteroid substrate. Knowledge of the position of this water molecule, combined with the stereochemistry of hydride transfer, suggests that the alpha face of a bound steroid will be oriented toward the side of the apolar cleft containing Trp 86.

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Primary Citation of related structures