Abstract
Dihydropyrimidinase, a dimetalloenzyme containing a carboxylated lysine within the active site, is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase, hydantoinase, and imidase. Unlike all known dihydropyrimidinases, which are tetrameric, pseudomonal dihydropyrimidinase forms a dimer at neutral pH. In this paper, we report the crystal structure of P. aeruginosa dihydropyrimidinase at pH 5.9 (PDB entry 5YKD). The crystals of P. aeruginosa dihydropyrimidinase belonged to space group C2221 with cell dimensions of a = 108.9, b = 155.7, and c = 235.6 Å. The structure of P. aeruginosa dihydropyrimidinase was solved at 2.17 Å resolution. An asymmetric unit of the crystal contained four crystallographically independent P. aeruginosa dihydropyrimidinase monomers. Gel filtration chromatographic analysis of purified P. aeruginosa dihydropyrimidinase revealed a mixture of dimers and tetramers at pH 5.9. Thus, P. aeruginosa dihydropyrimidinase can form a stable tetramer both in the crystalline state and in the solution. Based on sequence analysis and structural comparison of the dimer-dimer interface between P. aeruginosa dihydropyrimidinase and Thermus sp. dihydropyrimidinase, different oligomerization mechanisms are proposed.
Highlights
Dihydropyrimidinase is a key enzyme for pyrimidine catabolism [1, 2]
The crystal structure of P. aeruginosa PAO1 dihydropyrimidinase indicated that several residues crucial for tetramerization are not found in P. aeruginosa dihydropyrimidinase [28]
All data integration and scaling were carried out using HKL-2000 [30]. ere were four P. aeruginosa dihydropyrimidinase monomers per asymmetric unit. e crystal structure of P. aeruginosa dihydropyrimidinase was solved at 2.17 Aresolution with the molecular replacement software AMoRe [31] using the dihydropyrimidinase (PDB entry 5E5C) [28] as
Summary
Received 17 October 2017; Revised 20 November 2017; Accepted 3 December 2017; Published 30 January 2018. Dihydropyrimidinase, a dimetalloenzyme containing a carboxylated lysine within the active site, is a member of the cyclic amidohydrolase family, which includes allantoinase, dihydroorotase, hydantoinase, and imidase. We report the crystal structure of P. aeruginosa dihydropyrimidinase at pH 5.9 (PDB entry 5YKD). E crystals of P. aeruginosa dihydropyrimidinase belonged to space group C2221 with cell dimensions of a 108.9, b 155.7, and c 235.6 A . E structure of P. aeruginosa dihydropyrimidinase was solved at 2.17 Aresolution. An asymmetric unit of the crystal contained four crystallographically independent P. aeruginosa dihydropyrimidinase monomers. Gel filtration chromatographic analysis of purified P. aeruginosa dihydropyrimidinase revealed a mixture of dimers and tetramers at pH 5.9. Us, P. aeruginosa dihydropyrimidinase can form a stable tetramer both in the crystalline state and in the solution. Based on sequence analysis and structural comparison of the dimer-dimer interface between P. aeruginosa dihydropyrimidinase and ermus sp. Based on sequence analysis and structural comparison of the dimer-dimer interface between P. aeruginosa dihydropyrimidinase and ermus sp. dihydropyrimidinase, different oligomerization mechanisms are proposed
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