1GKR

L-Hydantoinase (Dihydropyrimidinase) from Arthrobacter aurescens

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The structure of L-hydantoinase from Arthobacter aurescens leads to an understanding of dihydropyrimidinase substrate and enantio specificity.

Abendroth, J., Niefind, K., May, O., Siemann, M., Syldatk, C., Schomburg, D.

(2002) Biochemistry 41: 8589-8597

  • DOI: 10.1021/bi0157722
  • Primary Citation of Related Structures:  
    1GKR

  • PubMed Abstract: 

    • L-Hydantoinase from Arthrobacter aurescens (L-Hyd) is a member of the dihydropyrimidinases which in turn belong to the cyclic amidases. Dihydropyrimidinases catalyze the reversible hydrolytic ring opening of dihydropyrimidines as the second step in the catabolism of pyrimidines ...

    L-Hydantoinase from Arthrobacter aurescens (L-Hyd) is a member of the dihydropyrimidinases which in turn belong to the cyclic amidases. Dihydropyrimidinases catalyze the reversible hydrolytic ring opening of dihydropyrimidines as the second step in the catabolism of pyrimidines. In biotechnology, their hydroloytic activity on five-membered cyclic diamides (hydantoins) is used in the enantio-specific production of amino acids from racemic hydantoins. L-Hyd differs from most of the other dihydropyrimidinases by an L-enantio specificity and by lacking activity on possible natural substrates such as dihydropyrimidines. In this paper, we describe the three-dimensional structure of L-Hyd which was solved by molecular replacement using a homology model and subsequently refined to 2.6 A resolution. Each subunit of the tetrameric L-Hyd consists of an elliptically distorted (alpha/beta)(8)-barrel domain, which hosts the active site, and a beta-sheet domain. In the active site, a binuclear zinc center activates a water molecule for nucleophilic attack on the substrates' amide bond. L-Hyd shows a strong homology both in fold and in metal coordination in the active site to another dihydropyrimidinase from Thermus sp. (D-hydantoinase) and to a slightly lesser degree to ureases, dihydroorotase and phosphotriesterase. Using the homology to ureases, a model for the transition state was modeled in the active site of L-Hyd and D-hydantoinase. This model could provide an explanation for the different substrate and enantio selectivities of both dihydropyrimidinases.

    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of a Hydantoinase from Arthrobacter Aurescens Dsm 3745.
      May, O., Siemann, M., Syldatk, C., Niefind, K., Schomburg, D.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 1209
    Organizational Affiliation: 

    Institut für Biochemie, Universität zu Köln, Zülpicher Strasse 47, 50674 Köln, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NON-ATP DEPENDENT L-SELECTIVE HYDANTOINASEA, B, C, D458Paenarthrobacter aurescensMutation(s): 1 
Gene Names: lhyD
EC: 3.5.2.2 (PDB Primary Data), 3.5.2 (UniProt)
UniProt
Find proteins for P81006 (Paenarthrobacter aurescens)
Explore P81006 
Go to UniProtKB:  P81006
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81006
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX		A, B, C, D L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.5α = 90
b = 74.3β = 106.57
c = 146.9γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XENGENdata reduction
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-09
    Changes: Data collection, Database references, Derived calculations, Other