5EPO

The three-dimensional structure of Clostridium absonum 7alpha-hydroxysteroid dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The three-dimensional structure of Clostridium absonum 7 alpha-hydroxysteroid dehydrogenase: new insights into the conserved arginines for NADP(H) recognition

Lou, D.Wang, B.Tan, J.Zhu, L.Cen, X.Ji, Q.Wang, Y.

(2016) Sci Rep 6: 22885-22885

  • DOI: 10.1038/srep22885

  • PubMed Abstract: 
  • 7α-hydroxysteroid dehydrogenase (7α-HSDH) can catalyse the oxidation of C7 α-OH of the steroid nucleus in the bile acid metabolism. In the paper we determined the crystal structure of 7α-HSDH from Clostridium absonum (CA 7α-HSDH) complexed with tauro ...

    7α-hydroxysteroid dehydrogenase (7α-HSDH) can catalyse the oxidation of C7 α-OH of the steroid nucleus in the bile acid metabolism. In the paper we determined the crystal structure of 7α-HSDH from Clostridium absonum (CA 7α-HSDH) complexed with taurochenodeoxycholic acid (TCDCA) and NADP(+) by X-ray diffraction, which, as a tetramer, possesses the typical α/β folding pattern. The four subunits of an asymmetric unit lie in the fact that there are the stable hydrophobic interactions between Q-axis-related subunits. Significantly, we captured an active state of the NADP(+), confirming that nicotinamide moiety of NADP(+) act as electron carrier in the dehydrogenation. On the basis of crystal structure analysis, site-directed mutagenesis and MD simulation, furthermore, we find that the guanidinium of Arg38 can form the stable cation-π interaction with the adenine ring of NADP(+), and the cation-π interaction and hydrogen bonds between Arg38 and NADP(+) have a significant anchor effect on the cofactor binding to CA 7α-HSDH.


    Organizational Affiliation

    Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
7-alpha-hydroxysteroid deydrogenase
A, B, C, D
262Clostridium sardinienseMutation(s): 0 
Find proteins for G9FRD7 (Clostridium sardiniense)
Go to UniProtKB:  G9FRD7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
TUD
Query on TUD

Download SDF File 
Download CCD File 
A, B, C, D
TAUROCHENODEOXYCHOLIC ACID
2-(((3ALPHA,5BETA,7ALPHA)-3,7-DIHYDROXY-24-OXOCHOLAN-24-YL)AMINO)ETHANESULFONIC ACID; TAUROCHENODEOXYCHOLATE
C26 H45 N O6 S
BHTRKEVKTKCXOH-BJLOMENOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.180α = 90.00
b = 69.680β = 90.00
c = 220.390γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China2014ZX09301306-007

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Data collection, Derived calculations