1AHI

7 ALPHA-HYDROXYSTEROID DEHYDROGENASE COMPLEXED WITH NADH AND 7-OXO GLYCOCHENODEOXYCHOLIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of the binary and ternary complexes of 7 alpha-hydroxysteroid dehydrogenase from Escherichia coli.

Tanaka, N.Nonaka, T.Tanabe, T.Yoshimoto, T.Tsuru, D.Mitsui, Y.

(1996) Biochemistry 35: 7715-7730

  • DOI: 10.1021/bi951904d
  • Primary Citation of Related Structures:  1AHH, 1FMC

  • PubMed Abstract: 
  • 7 alpha-Hydroxysteroid dehydrogenase (7 alpha-HSDH;1 EC 1.1.1.159) is an NAD+-dependent oxidoreductase belonging to the short-chain dehydrogenase/reductase (SDR) 1 family. It catalyzes the dehydrogenation of a hydroxyl group at position 7 of the ster ...

    7 alpha-Hydroxysteroid dehydrogenase (7 alpha-HSDH;1 EC 1.1.1.159) is an NAD+-dependent oxidoreductase belonging to the short-chain dehydrogenase/reductase (SDR) 1 family. It catalyzes the dehydrogenation of a hydroxyl group at position 7 of the steroid skeleton of bile acids. The crystal structure of the binary (complexed with NAD+) complex of 7 alpha-HSDH has been solved at 2.3 A resolution by the multiple isomorphous replacement method. The structure of the ternary complex [the enzyme complexed with NADH, 7-oxoglycochenodeoxycholic acid (as a reaction product), and possibly partially glycochenodeoxycholic acid (as a substrate)] has been determined by a difference Fourier method at 1.8 A resolution. The enzyme 7 alpha-HSDH is an alpha/beta doubly wound protein having a Rossmann-fold domain for NAD (H) binding. Upon substrate binding, large conformation changes occur at the substrate binding loop (between the beta F strand and alpha G helix) and the C-terminal segment (residues 250-255). The variable amino acid sequences of the substrate-binding loop appear to be responsible for the wide variety of substrate specificities observed among the enzymes of the SDR family. The crystal structure of the ternary complex of 7 alpha-HSDH, which is the only structure available as the ternary complex among the enzymes of the SDR family, indicates that the highly conserved Tyr159 and Ser146 residues most probably directly interact with the hydroxyl group of the substrates although this observation cannot be definite due to an insufficiently characterized nature of the ternary complex. The strictly conserved Lys163 is hydrogen-bonded to both the 2'- and 3'-hydroxyl groups of the nicotinamide ribose of NAD(H). We propose a new catalytic mechanism possibly common to all the enzymes belonging to the SDR family in which a tyrosine residue (Tyr159) acts as a catalytic base and a serine residue (Ser146) plays a subsidiary role of stabilizing substrate binding.


    Related Citations: 
    • Cloning and Sequencing of the 7 Alpha-Hydroxysteroid Dehydrogenase Gene from Escherichia Coli Hb101 and Characterization of the Expressed Enzyme
      Yoshimoto, T.,Higashi, H.,Kanatani, A.,Lin, X.S.,Nagai, H.,Oyama, H.,Kurazono, K.,Tsuru, D.
      (1991) J.Bacteriol. 173: 2173
    • Crystallization and Preliminary X-Ray Crystallographic Studies of 7Alpha-Hydroxysteroid Dehydrogenase from Escherichia Coli
      Tanaka, N.,Nonaka, T.,Yoshimoto, T.,Tsuru, D.,Mitsui, Y.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of BioEngineering, Nagaoka University of Technology, Niigata, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
7 ALPHA-HYDROXYSTEROID DEHYDROGENASE
A, B
255Escherichia coli (strain K12)Gene Names: hdhA (hsdH)
EC: 1.1.1.159
Find proteins for P0AET8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AET8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CHO
Query on CHO

Download SDF File 
Download CCD File 
A, B
GLYCOCHENODEOXYCHOLIC ACID
C26 H43 N O5
GHCZAUBVMUEKKP-GYPHWSFCSA-N
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A, B
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.180 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.590α = 90.00
b = 81.590β = 90.00
c = 214.650γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
PROCESSdata reduction
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2013-10-30
    Type: Non-polymer description