Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1: Insights into the molecular basis of formation of a dimer

Tzeng, C.T.; Huang, Yen‐Hua; Huang, Cheng-Yang

doi:10.1016/j.bbrc.2016.08.144

Cited by 20 publications

(21 citation statements)

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“…It was noted that the crystals of the dimeric P. aeruginosa dihydropyrimidinase belonged to space group P 3 1 21 grown at the condition of 28% PEG 6000, 100 mM HEPES, 200 mM lithium acetate, pH 7.5 [ 28 ]. Due to the different crystallization condition, we attempted to test whether the oligomerization of P. aeruginosa dihydropyrimidinase is pH-dependent.…”

Section: Resultsmentioning

confidence: 99%

“…All known dihydropyrimidinases are tetramers. However, pseudomonal dihydropyrimidinase/hydantoinase forms a dimer at neutral pH [ 26 – 28 ]. Given that the structure implies that P. aeruginosa dihydropyrimidinase may also form a tetramer in the crystalline state at pH 5.9 ( Figure 2 ), we performed biochemical verification to confirm the oligomerization state.…”

Section: Resultsmentioning

confidence: 99%

“…There were four P. aeruginosa dihydropyrimidinase monomers per asymmetric unit. The crystal structure of P. aeruginosa dihydropyrimidinase was solved at 2.17 Å resolution with the molecular replacement software AMoRe [ 31 ] using the dihydropyrimidinase (PDB entry 5E5C) [ 28 ] as model. After molecular replacement, model building was carried out using XtalView [ 32 ].…”

Section: Methodsmentioning

confidence: 99%

“…putida YZ-26 functions as a dimer [ 26 , 27 ]. Recently, we identified that dihydropyrimidinase from P. aeruginosa PAO1 also forms a dimer [ 28 ]. In addition, the crystal structure of P. aeruginosa PAO1 dihydropyrimidinase indicated that several residues crucial for tetramerization are not found in P. aeruginosa dihydropyrimidinase [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

“…Recently, we identified that dihydropyrimidinase from P. aeruginosa PAO1 also forms a dimer [ 28 ]. In addition, the crystal structure of P. aeruginosa PAO1 dihydropyrimidinase indicated that several residues crucial for tetramerization are not found in P. aeruginosa dihydropyrimidinase [ 28 ]. In this study, we found that the oligomerization of P. aeruginosa PAO1 dihydropyrimidinase is a pH-dependent process.…”

Section: Introductionmentioning

confidence: 99%

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Structural Basis for pH-Dependent Oligomerization of Dihydropyrimidinase fromPseudomonas aeruginosaPAO1

Cheng

Huang

2018

Bioinorganic Chemistry and Applications

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%