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Molecular Structure of D-Hydantoinase from a Bacillus sp. AR9: Evidence for mercury inhibition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular structure of D-hydantoinase from Bacillus sp. AR9: evidence for mercury inhibition.

Radha Kishan, K.V.Vohra, R.M.Ganesan, K.Agrawal, V.Sharma, V.M.Sharma, R.

(2005) J.Mol.Biol. 347: 95-105

  • DOI: 10.1016/j.jmb.2005.01.025

  • PubMed Abstract: 
  • Stereospecific conversion of hydantoins into their carbamoyl acid derivatives could be achieved by using the enzyme hydantoinase. Specific hydantoinases convert either the D-form or the L-form of the hydantoin and the amino acids responsible for ster ...

    Stereospecific conversion of hydantoins into their carbamoyl acid derivatives could be achieved by using the enzyme hydantoinase. Specific hydantoinases convert either the D-form or the L-form of the hydantoin and the amino acids responsible for stereospecificity have not been identified. Structural studies on hydantoinases from a few bacterial species were published recently. The structure of a thermostable D-hydantoinase from Bacillus sp. AR9 (bar9HYD) was solved to 2.3 angstroms resolution. The usual modification of carboxylation of the active-site residue Lys150 did not happen in bar9HYD. Two manganese ions were modelled in the active site. Through biochemical studies, it was shown that mercury inhibits the activity of the enzyme. The mercury derivative provided some information about the binding site of the mercuric inhibitors and a possible reason for inhibition is presented.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction analysis of a thermostable D-hydantoinase from mesophilic Bacillus sp.AR9
      Agrawal, V.,Sharma, R.,Ganeshan, K.,Radha Kishan, K.V.
      (2002) Acta Crystallogr.,Sect.D 58: 2175


    Organizational Affiliation

    Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India. kishan@imtech.res.in




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-Hydantoinase
A, B
461Bacillus sp. AR9Mutation(s): 0 
EC: 3.5.2.2
Find proteins for Q5DLU2 (Bacillus sp. AR9)
Go to UniProtKB:  Q5DLU2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.199 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 129.540α = 90.00
b = 129.540β = 90.00
c = 102.850γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
MAR345data collection
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description