3QWI

Crystal structure of a 17beta-hydroxysteroid dehydrogenase (holo form) from fungus Cochliobolus lunatus in complex with NADPH and coumestrol

PDB DOI: https://doi.org/10.2210/pdb3QWI/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Curvularia lunata
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-02-28 Released: 2012-01-18
Deposition Author(s): Cassetta, A., Lamba, D., Krastanova, I., Stojan, J., Lanisnik Rizner, T., Kristan, K., Brunskole, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Free: 0.233
R-Value Work: 0.161
R-Value Observed: 0.165

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural studies on the flavonoid inhibition of a fungal 17Beta-Hydroxysteroid dehydrogenase

Cassetta, A., Krastanova, I., Kristan, K., Brunskole Svegelj, M., Lamba, D., Lanisnik Rizner, T., Stojan, J.

(2012) Biochem J 441: 151-160

PubMed: 21929506 Search on PubMed
DOI: https://doi.org/10.1042/BJ20110567
Primary Citation of Related Structures:
3QWF, 3QWI

PubMed Abstract:
The 17β-HSD (17β-hydroxysteroid dehydrogenase) from the filamentous fungus Cochliobolus lunatus (17β-HSDcl) is a NADP(H)-dependent enzyme that preferentially catalyses the interconversion of inactive 17-oxo-steroids and their active 17β-hydroxy counterparts. 17β-HSDcl belongs to the SDR (short-chain dehydrogenase/reductase) superfamily. It is currently the only fungal 17β-HSD member that has been described and represents one of the model enzymes of the cP1 classical subfamily of NADPH-dependent SDR enzymes. A thorough crystallographic analysis has been performed to better understand the structural aspects of this subfamily and provide insights into the evolution of the HSD enzymes. The crystal structures of the 17β-HSDcl apo, holo and coumestrol-inhibited ternary complex, and the active-site Y167F mutant reveal subtle conformational differences in the substrate-binding loop that probably modulate the catalytic activity of 17β-HSDcl. Coumestrol, a plant-derived non-steroidal compound with oestrogenic activity, inhibits 17β-HSDcl [IC50 2.8?μM; at 100?μM substrate (4-oestrene-3,17-dione)] by occupying the putative steroid-binding site. In addition to an extensive hydrogen-bonding network, coumestrol binding is stabilized further by π-π stacking interactions with Tyr212. A stopped-flow kinetic experiment clearly showed the coenzyme dissociation as the slowest step of the reaction and, in addition to the low steroid solubility, it prevents the accumulation of enzyme-coenzyme-steroid ternary complexes.

Organizational Affiliation

Istituto di Cristallografia - UOS Trieste, Consiglio Nazionale delle Ricerche, Area Science Park-Basovizza, S.S. 14 km 163.5, I-34149 Trieste, Italy. alberto.cassetta@ic.cnr.it

Macromolecule Content

Total Structure Weight: 120.08 kDa
Atom Count: 8,475
Modelled Residue Count: 1,041
Deposited Residue Count: 1,080
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
17beta-hydroxysteroid dehydrogenase	A, B, C, D	270	Curvularia lunata	Mutation(s): 0 Gene Names: 17HSDcl EC: 1.1.1.62
UniProt
Find proteins for O93874 (Cochliobolus lunatus) Explore O93874 Go to UniProtKB: O93874
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O93874
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain K [auth B]	E [auth A], K [auth B], M [auth C], P [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D]
CUE Query on CUE Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth D]	F [auth A], L [auth B], Q [auth D]	Coumestrol C₁₅ H₈ O₅ ZZIALNLLNHEQPJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	G [auth A] H [auth A] I [auth A] J [auth A] N [auth C] G [auth A], H [auth A], I [auth A], J [auth A], N [auth C], O [auth C], R [auth D], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Free: 0.233
R-Value Work: 0.161
R-Value Observed: 0.165
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 63.41	α = 90
b = 116.81	β = 103.14
c = 70.43	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-01-18
Type: Initial release
Version 1.1: 2013-07-03
Changes: Non-polymer description
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description