5GT9

The X-ray structure of 7beta-hydroxysteroid dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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This is version 1.1 of the entry. See complete history


Literature

Structure of NADP(+)-bound 7 beta-hydroxysteroid dehydrogenase reveals two cofactor-binding modes

Wang, R.Wu, J.Jin, D.K.Chen, Y.Lv, Z.Chen, Q.Miao, Q.Huo, X.Wang, F.

(2017) Acta Crystallogr F Struct Biol Commun 73: 246-252

  • DOI: https://doi.org/10.1107/S2053230X17004460
  • Primary Citation of Related Structures:  
    5GT9

  • PubMed Abstract: 

    In mammals, bile acids/salts and their glycine and taurine conjugates are effectively recycled through enterohepatic circulation. 7β-Hydroxysteroid dehydrogenases (7β-HSDHs; EC 1.1.1.201), including that from the intestinal microbe Collinsella aerofaciens, catalyse the NADPH-dependent reversible oxidation of secondary bile-acid products to avoid potential toxicity. Here, the first structure of NADP + bound to dimeric 7β-HSDH is presented. In one active site, NADP + adopts a conventional binding mode similar to that displayed in related enzyme structures. However, in the other active site a unique binding mode is observed in which the orientation of the nicotinamide is different. Since 7β-HSDH has become an attractive target owing to the wide and important pharmaceutical use of its product ursodeoxycholic acid, this work provides a more detailed template to support rational protein engineering to improve the enzymatic activities of this useful biocatalyst, further improving the yield of ursodeoxycholic acid and its other applications.


  • Organizational Affiliation

    Wuxi Biortus Biosciences Co. Ltd, A5, 6 Dongsheng West Road, 214437 Jiangyin, Jiangsu, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxidoreductase, short chain dehydrogenase/reductase family protein
A, B
263Collinsella aerofaciens ATCC 25986Mutation(s): 0 
Gene Names: COLAER_02088
UniProt
Find proteins for A4ECA9 (Collinsella aerofaciens (strain ATCC 25986 / DSM 3979 / JCM 10188 / KCTC 3647 / NCTC 11838 / VPI 1003))
Explore A4ECA9 
Go to UniProtKB:  A4ECA9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ECA9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NAP Binding MOAD:  5GT9 Ka: 4.47e+4 (M^-1) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.73α = 90
b = 72.73β = 90
c = 171.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata processing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Jiangsu Innovation fund for Technology-based FirmsChinaBC2013062
Torch High Technology Industry Development Center, Ministry of Science and Technology, ChinaChina2015GH581522

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description