PDBsum entry 5e5c

Hydrolase

PDB id: 5e5c

Contents

Protein chains

478 a.a.

Metals

_ZN ×4

Waters ×338

PDB id:

5e5c

Name:

Hydrolase

Title:

Crystal structure of dihydropyrimidinase from pseudomonas aeruginosa pao1

Structure:

D-hydantoinase/dihydropyrimidinase. Chain: a, c. Synonym: dhpase. Engineered: yes

Source:

Pseudomonas aeruginosa (strain atcc 15692 / pao1 / 1c / prs 101 / lmg 12228). Organism_taxid: 208964. Strain: atcc 15692 / pao1 / 1c / prs 101 / lmg 12228. Gene: dht, pa0441. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.172 R-free: 0.215

Authors:

C.C.Huang,Y.H.Huang,Y.C.Hsieh,C.T.Tzeng,C.J.Chen,C.Y.Huang

Key ref:

C.T.Tzeng et al. (2016). Crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1: Insights into the molecular basis of formation of a dimer. Biochem Biophys Res Commun, 478, 1449-1455. PubMed id: 27576201 DOI: 10.1016/j.bbrc.2016.08.144

Date:

08-Oct-15 Release date: 21-Sep-16

Protein chains

Q9I676  (HYDA_PSEAE) -  D-hydantoinase/dihydropyrimidinase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 479 a.a.

Struc: 478 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.5.2.2 - dihydropyrimidinase.
• Reaction: 5,6-dihydrouracil + H2O = 3-(carbamoylamino)propanoate + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1016/j.bbrc.2016.08.144

Biochem Biophys Res Commun 478:1449-1455 (2016)

PubMed id: 27576201

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

C.T.Tzeng, Y.H.Huang, C.Y.Huang.

ABSTRACT

Dihydropyrimidinase, a tetrameric metalloenzyme, is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase, hydantoinase, and imidase. In this paper, we report the crystal structure of dihydropyrimidinase from Pseudomonas aeruginosa PAO1 at 2.1 Å resolution. The structure of P. aeruginosa dihydropyrimidinase reveals a classic (β/α)8-barrel structure core embedding the catalytic dimetal center and a β-sandwich domain, which is commonly found in the architecture of dihydropyrimidinases. In contrast to all dihydropyrimidinases, P. aeruginosa dihydropyrimidinase forms a dimer, rather than a tetramer, both in the crystalline state and in the solution. Basing on sequence analysis and structural comparison of the C-terminal region and the dimer-dimer interface between P. aeruginosa dihydropyrimidinase and Thermus sp. dihydropyrimidinase, we propose a working model to explain why this enzyme cannot be a tetramer.