5YKD

Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 at 2.17 angstrom resolution

Summary for 5YKD

• Entry DOI: 10.2210/pdb5ykd/pdb
• Descriptor: D-hydantoinase/dihydropyrimidinase, ZINC ION (3 entities in total)
• Functional Keywords: dihydropyrimidinase, hydrolase
• Biological source: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
• Total number of polymer chains: 4
• Total formula weight: 209786.65

Authors

Huang, Y.H.,Huang, C.Y. (deposition date: 2017-10-14, release date: 2018-02-21, Last modification date: 2023-11-22)

Primary citation

Cheng, J.H.,Huang, C.C.,Huang, Y.H.,Huang, C.Y.
Structural Basis for pH-Dependent Oligomerization of Dihydropyrimidinase fromPseudomonas aeruginosaPAO1.
Bioinorg Chem Appl, 2018:9564391-9564391, 2018

PubMed 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 dihydropyrimidinase at pH 5.9 (PDB entry 5YKD). The crystals of dihydropyrimidinase belonged to space group 222 with cell dimensions of  = 108.9,  = 155.7, and  = 235.6 Å. The structure of dihydropyrimidinase was solved at 2.17 Å resolution. An asymmetric unit of the crystal contained four crystallographically independent dihydropyrimidinase monomers. Gel filtration chromatographic analysis of purified dihydropyrimidinase revealed a mixture of dimers and tetramers at pH 5.9. Thus, 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 dihydropyrimidinase and sp. dihydropyrimidinase, different oligomerization mechanisms are proposed.

PubMed: 29666631
DOI: 10.1155/2018/9564391

Experimental method

X-RAY DIFFRACTION (2.17 Å)