Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 199.30 kDa 
• Atom Count: 14196 
• Modelled Residue Count: 1804 
• Deposited Residue Count: 1832 
• Unique protein chains: 1

1GKR

L-Hydantoinase (Dihydropyrimidinase) from Arthrobacter aurescens

• DOI: 10.2210/pdb1GKR/pdb

• Classification: HYDROLASE
• Organism(s): Paenarthrobacter aurescens
• Mutation(s): Yes 


• Deposited: 2001-08-20 Released: 2002-07-25 
• Deposition Author(s): Abendroth, J., Niefind, K., Schomburg, D.

---

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 

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

• PubMed: 12093275 
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NON-ATP DEPENDENT L-SELECTIVE HYDANTOINASE	A, B, C, D	458	Paenarthrobacter aurescens	Mutation(s): 1  Gene Names: lhyD EC: 3.5.2.2 (PDB Primary Data), 3.5.2 (UniProt)
Find proteins for P81006 (Paenarthrobacter aurescens) Explore P81006  Go to UniProtKB:  P81006

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

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 = 111.5	α = 90
b = 74.3	β = 106.57
c = 146.9	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XENGEN	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-08-20 
• Released Date: 2002-07-25 
Deposition Author(s): Abendroth, J., Niefind, K., Schomburg, D.

Revision History  

• 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