PDBsum entry 4lcs

Hydrolase activator

PDB id: 4lcs

Contents

Protein chain

485 a.a.

Ligands

HYN

Metals

_ZN ×2

Waters ×170

PDB id:

4lcs

Name:

Hydrolase activator

Title:

The crystal structure of di-zn dihydropyrimidinase in complex with hydantoin

Structure:

Chromosome 8 scaf14545, whole genome shotgun sequence. Chain: a. Synonym: dihydropyrimidinase. Engineered: yes

Source:

Tetraodon nigroviridis. Spotted green pufferfish. Organism_taxid: 99883. Gene: dpys, gsteng00015639001. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.168 R-free: 0.202

Authors:

Y.C.Hsieh,M.C.Chen,C.C.Hsu,S.I.Chan,Y.S.Yang

Key ref:

Y.C.Hsieh et al. (2013). Crystal structures of vertebrate dihydropyrimidinase and complexes from Tetraodon nigroviridis with lysine carbamylation: metal and structural requirements for post-translational modification and function. J Biol Chem, 288, 30645-30658. PubMed id: 24005677 DOI: 10.1074/jbc.M113.496778

Date:

23-Jun-13 Release date: 18-Sep-13

Protein chain

Q4SMR4  (Q4SMR4_TETNG) -  Dihydropyrimidinase from Tetraodon nigroviridis

Seq: 500 a.a.

Struc: 485 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DOI no: 10.1074/jbc.M113.496778

J Biol Chem 288:30645-30658 (2013)

PubMed id: 24005677

Crystal structures of vertebrate dihydropyrimidinase and complexes from Tetraodon nigroviridis with lysine carbamylation: metal and structural requirements for post-translational modification and function.

Y.C.Hsieh, M.C.Chen, C.C.Hsu, S.I.Chan, Y.S.Yang, C.J.Chen.

ABSTRACT

Lysine carbamylation, a post-translational modification, facilitates metal coordination for specific enzymatic activities. We have determined structures of the vertebrate dihydropyrimidinase from Tetraodon nigroviridis (TnDhp) in various states: the apoenzyme as well as two forms of the holoenzyme with one and two metals at the catalytic site. The essential active-site structural requirements have been identified for the possible existence of four metal-mediated stages of lysine carbamylation. Only one metal is sufficient for stabilizing lysine carbamylation; however, the post-translational lysine carbamylation facilitates additional metal coordination for the regulation of specific enzymatic activities through controlling the conformations of two dynamic loops, Ala(69)-Arg(74) and Met(158)-Met(165), located in the tunnel for the substrate entrance. The substrate/product tunnel is in the "open form" in the apo-TnDhp, in the "intermediate state" in the monometal TnDhp, and in the "closed form" in the dimetal TnDhp structure, respectively. Structural comparison also suggests that the C-terminal tail plays a role in the enzymatic function through interactions with the Ala(69)-Arg(74) dynamic loop. In addition, the structures of the dimetal TnDhp in complexes with hydantoin, N-carbamyl-β-alanine, and N-carbamyl-β-amino isobutyrate as well as apo-TnDhp in complex with a product analog, N-(2-acetamido)-iminodiacetic acid, have been determined. These structural results illustrate how a protein exploits unique lysines and the metal distribution to accomplish lysine carbamylation as well as subsequent enzymatic functions.