Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PQS (software)

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 75.92 kDa 
• Atom Count: 5998 
• Modelled Residue Count: 642 
• Deposited Residue Count: 642 
• Unique protein chains: 1

2IPJ

Crystal structure of h3alpha-hydroxysteroid dehydrogenase type 3 mutant Y24A in complex with NADP+ and epi-testosterone

• PDB DOI: 10.2210/pdb2IPJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-10-12 Released: 2007-06-19 
• Deposition Author(s): Faucher, F., Cantin, L., Pereira de Jesus-Tran, K., Luu-the, V., Labrie, F., Breton, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.204 

Literature

Mouse 17alpha-Hydroxysteroid Dehydrogenase (AKR1C21) Binds Steroids Differently from other Aldo-keto Reductases: Identification and Characterization of Amino Acid Residues Critical for Substrate Binding.

Faucher, F., Cantin, L., Pereira de Jesus-Tran, K., Lemieux, M., Luu-The, V., Labrie, F., Breton, R.

(2007) J Mol Biol 369: 525-540

• PubMed: 17442338 
• DOI: 10.1016/j.jmb.2007.03.058
• Primary Citation of Related Structures:  
  2IPF, 2IPG, 2IPJ


• PubMed Abstract: 
  

The mouse 17alpha-hydroxysteroid dehydrogenase (m17alpha-HSD) is the unique known member of the aldo-keto reductase (AKR) superfamily able to catalyze efficiently and in a stereospecific manner the conversion of androstenedione (Delta4) into epi-testosterone (epi-T), the 17alpha-epimer of testosterone. Structural and mutagenic studies had already identified one of the residues delineating the steroid-binding cavity, A24, as the major molecular determinant for the stereospecificity of m17alpha-HSD. We report here a ternary complex crystal structure (m17alpha-HSD:NADP(+):epi-T) determined at 1.85 A resolution that confirms this and reveals a unique steroid-binding mode for an AKR enzyme. Indeed, in addition to the interactions found in all other AKRs (van der Waals contacts stabilizing the core of the steroid and the hydrogen bonds established at the catalytic site by the Y55 and H117 residues with the oxygen atom of the ketone group to be reduced), m17alpha-HSD establishes with the other extremity of the steroid nucleus an additional interaction involving K31. By combining direct mutagenesis and kinetic studies, we found that the elimination of this hydrogen bond did not affect the affinity of the enzyme for its steroid substrate but led to a slight but significant increase of its catalytic efficiency (k(cat)/K(m)), suggesting a role for K31 in the release of the steroidal product at the end of the reaction. This previously unobserved steroid-binding mode for an AKR is similar to that adopted by other steroid-binding proteins, the hydroxysteroid dehydrogenases of the short-chain dehydrogenases/reductases (SDR) family and the steroid hormone nuclear receptors. Mutagenesis and structural studies made on the human type 3 3alpha-HSD, a closely related enzyme that shares 73% amino acids identity with the m17alpha-HSD, also revealed that the residue at position 24 of these two enzymes directly affects the binding and/or the release of NADPH, in addition to its role in their 17alpha/17beta stereospecificity.

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Organizational Affiliation: 

Oncology and Molecular Endocrinology Research Center, Laval University Medical Center (CHUL), Laval University, Québec, Canada G1V 4G2.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldo-keto reductase family 1 member C2	A, B	321	Homo sapiens	Mutation(s): 0  Gene Names: AKR1C2, DDH2 EC: 1 (PDB Primary Data), 1.3.1.20 (PDB Primary Data), 1.1.1.213 (PDB Primary Data), 1.1.1.112 (UniProt), 1.1.1.209 (UniProt), 1.1.1.53 (UniProt), 1.1.1.62 (UniProt), 1.1.1.357 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P52895 (Homo sapiens) Explore P52895  Go to UniProtKB:  P52895
PHAROS:  P52895 GTEx:  ENSG00000151632

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	D [auth A], M [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
FFA	E [auth A], N [auth B]	(10ALPHA,13ALPHA,14BETA,17ALPHA)-17-HYDROXYANDROST-4-EN-3-ONE C19 H28 O2 MUMGGOZAMZWBJJ-KZYORJDKSA-N
SO4	C [auth A], K [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	F [auth A], G [auth A], O [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], J [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.204 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.788	α = 90
b = 144.788	β = 90
c = 203.885	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-12 
• Released Date: 2007-06-19 
Deposition Author(s): Faucher, F., Cantin, L., Pereira de Jesus-Tran, K., Luu-the, V., Labrie, F., Breton, R.

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2012-05-16
  Changes: Other
• Version 1.4: 2018-01-24
  Changes: Structure summary