1GKP

D-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space group C2221


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-Ray Structure of a Dihydropyrimidinase from Thermus Sp. At 1.3 A Resolution

Abendroth, J.Niefind, K.Schomburg, D.

(2002) J Mol Biol 320: 143

  • DOI: 10.1016/S0022-2836(02)00422-9
  • Primary Citation of Related Structures:  
    1GKQ, 1GKP

  • PubMed Abstract: 
  • Dihydropyrimidinases (hydantoinases) catalyse the reversible hydrolytic ring-opening of cyclic diamides such as dihydropyrimidines in the catabolism of pyrimidines. In biotechnology, these enzymes find application in the enantiospecific production of amino acids from racemic hydantoins ...

    Dihydropyrimidinases (hydantoinases) catalyse the reversible hydrolytic ring-opening of cyclic diamides such as dihydropyrimidines in the catabolism of pyrimidines. In biotechnology, these enzymes find application in the enantiospecific production of amino acids from racemic hydantoins. The crystal structure of a D-enantio-specific dihydropyrimidinase from Thermus sp. (D-hydantoinase) was solved de novo by multiwavelength anomalous diffraction phasing. In spite of a large unit cell the D-hydantoinase crystals exhibit excellent diffraction properties. The structure was subsequently refined at 1.30 A resolution against native data. The core of D-hydantoinase consists of a (alpha/beta)(8)-barrel, which is flanked by a beta-sheet domain and some additional helices. In the active site, a carboxylated lysine residue and the catalytically active hydroxide ion bridge a binuclear zinc centre. The tertiary structure and shape of the active site show strong homology to that of ureases, dihydroorotases, and phosphotriesterases. The homology of the active site was exploited for in silicio docking of substrates in the active site. This could shed light both on the substrate binding in hydantoinases and on the recently highly discussed origin of the proton in the course of hydantoinase catalysis.


    Related Citations: 
    • Crystallization, Preliminary X-Ray Analysis of a Native and Selenomethionine D-Hydantoinase from Thermus Sp
      Abendroth, J., Niefind, K., Schomburg, D.
      (2000) Acta Crystallogr D Biol Crystallogr D56: 1166

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYDANTOINASEA, B, C, D, E, F458Thermus sp.Mutation(s): 1 
EC: 3.5.2.2
Find proteins for Q7SIE9 (Thermus sp)
Explore Q7SIE9 
Go to UniProtKB:  Q7SIE9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
CA [auth F], T [auth D]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth F] , I [auth A] , L [auth B] , O [auth C] , P [auth C] , S [auth D] , W [auth E] , X [auth E] , 
BA [auth F],  I [auth A],  L [auth B],  O [auth C],  P [auth C],  S [auth D],  W [auth E],  X [auth E],  Y [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth F] , G [auth A] , H [auth A] , J [auth B] , K [auth B] , M [auth C] , N [auth C] , Q [auth D] , 
AA [auth F],  G [auth A],  H [auth A],  J [auth B],  K [auth B],  M [auth C],  N [auth C],  Q [auth D],  R [auth D],  U [auth E],  V [auth E],  Z [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E, FL-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.2α = 90
b = 215.9β = 90
c = 207.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
PROWdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMphasing
ARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-27
    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: 2019-07-24
    Changes: Data collection, Derived calculations