1YNY | pdb_00001yny

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

• PDB DOI: https://doi.org/10.2210/pdb1YNY/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. AR9
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-26 Released: 2005-03-01 
• Deposition Author(s): Radha Kishan, K.V., Vohra, R.M., Ganeshan, K., Agrawal, V., Sharma, V.M., Sharma, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.243 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 

Starting Model: experimental

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 Biology 347: 95-105

• PubMed: 15733920 
• DOI: https://doi.org/10.1016/j.jmb.2005.01.025
• Primary Citation Related Structures: 
  1YNY


• 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 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.

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Organizational Affiliation: 
• Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 101.16 kDa 
• Atom Count: 7,333 
• Modeled Residue Count: 914 
• Deposited Residue Count: 922 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-Hydantoinase	A, B	461	Bacillus sp. AR9	Mutation(s): 0  EC: 3.5.2.2
UniProt
Find proteins for Q5DLU2 (Bacillus sp. AR9) Explore Q5DLU2  Go to UniProtKB:  Q5DLU2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth A], E [auth B], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.243 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.54	α = 90
b = 129.54	β = 90
c = 102.85	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Radha Kishan, K.V., Vohra, R.M., Ganeshan, K., Agrawal, V., Sharma, V.M., Sharma, R.

Revision History  

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description