2HEZ | pdb_00002hez

Bifidobacterium longum bile salt hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.216 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2HEZ

This is version 1.4 of the entry. See complete history

Literature

Structural and Functional Analysis of a Conjugated Bile Salt Hydrolase from Bifidobacterium longum Reveals an Evolutionary Relationship with Penicillin V Acylase.

Kumar, R.S.Brannigan, J.A.Prabhune, A.A.Pundle, A.V.Dodson, G.G.Dodson, E.J.Suresh, C.G.

(2006) J Biological Chem 281: 32516-32525

  • DOI: https://doi.org/10.1074/jbc.M604172200
  • Primary Citation Related Structures: 
    2HEZ, 2HF0

  • PubMed Abstract: 

    Bile salt hydrolase (BSH) is an enzyme produced by the intestinal microflora that catalyzes the deconjugation of glycine- or taurine-linked bile salts. The crystal structure of BSH reported here from Bifidobacterium longum reveals that it is a member of N-terminal nucleophil hydrolase structural superfamily possessing the characteristic alphabetabetaalpha tetra-lamellar tertiary structure arrangement. Site-directed mutagenesis of the catalytic nucleophil residue, however, shows that it has no role in zymogen processing into its corresponding active form. Substrate specificity was studied using Michaelis-Menten and inhibition kinetics and fluorescence spectroscopy. These data were compared with the specificity profile of BSH from Clostridium perfrigens and pencillin V acylase from Bacillus sphaericus, for both of which the three-dimensional structures are available. Comparative analysis shows a gradation in activity toward common substrates, throwing light on a possible common route toward the evolution of pencillin V acylase and BSH.


  • Organizational Affiliation
    • Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008, India.

Macromolecule Content 

  • Total Structure Weight: 70.3 kDa 
  • Atom Count: 5,164 
  • Modeled Residue Count: 632 
  • Deposited Residue Count: 632 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bile salt hydrolase
A, B
316Bifidobacterium longumMutation(s): 1 
Gene Names: bsh
EC: 3.5.1.24 (PDB Primary Data), 3.5.1 (UniProt), 2.3.1 (UniProt), 3.5.1.74 (UniProt)
UniProt
Find proteins for Q9KK62 (Bifidobacterium longum)
Explore Q9KK62 
Go to UniProtKB:  Q9KK62
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KK62
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
A, B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.216 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.243α = 90
b = 125.243β = 90
c = 117.028γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-05
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection