1GKQ

D-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space group P212121

Summary for 1GKQ

• Entry DOI: 10.2210/pdb1gkq/pdb
• Related: 1GKP
• Descriptor: HYDANTOINASE, ZINC ION (3 entities in total)
• Functional Keywords: hydrolase, hydantoinase, dihydropyrimidinase, cyclic amidase
• Biological source: THERMUS SP.
• Total number of polymer chains: 4
• Total formula weight: 203648.96

Authors

Abendroth, J.,Niefind, K.,Schomburg, D. (deposition date: 2001-08-20, release date: 2002-06-27, Last modification date: 2023-12-13)

Primary citation

Abendroth, J.,Niefind, K.,Schomburg, D.
X-Ray Structure of a Dihydropyrimidinase from Thermus Sp. At 1.3 A Resolution
J.Mol.Biol., 320:143-, 2002

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. 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.

PubMed: 12079340
DOI: 10.1016/S0022-2836(02)00422-9

Experimental method

X-RAY DIFFRACTION (2.6 Å)