PDBsum entry 4c6c

Hydrolase

PDB id: 4c6c

Contents

Protein chain

362 a.a.

Ligands

FMT ×4

Metals

_ZN ×4

Waters ×375

PDB id:

4c6c

Name:

Hydrolase

Title:

Crystal structure of the dihydroorotase domain of human cad in apo- form obtained recombinantly from hek293 cells.

Structure:

Cad protein. Chain: a. Fragment: residues 1456-1846. Synonym: dihydroorotase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293.

Resolution:

1.45Å R-factor: 0.124 R-free: 0.148

Authors:

S.Ramon-Maiques,N.Lallous,A.Grande-Garcia

Key ref:

A.Grande-García et al. (2014). Structure, functional characterization, and evolution of the dihydroorotase domain of human CAD. Structure, 22, 185-198. PubMed id: 24332717 DOI: 10.1016/j.str.2013.10.016

Date:

18-Sep-13 Release date: 08-Jan-14

Protein chain

P27708  (PYR1_HUMAN) -  CAD protein from Homo sapiens

Seq: 2225 a.a.

Struc: 362 a.a.*

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

Enzyme reactions

• Enzyme class 2: E.C.2.1.3.2 - aspartate carbamoyltransferase.
• Pathway: Pyrimidine Biosynthesis
• Reaction: carbamoyl phosphate + L-aspartate = N-carbamoyl-L-aspartate + phosphate + H⁺
• Enzyme class 3: E.C.3.5.2.3 - dihydroorotase.

Pathway:

• Reaction: (S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate + H⁺
• Enzyme class 4: E.C.6.3.5.5 - carbamoyl-phosphate synthase (glutamine-hydrolyzing).

Pathway:

• Reaction: hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H⁺

hydrogencarbonate + L-glutamine + 2 × ATP (Bound ligand (Het Group name = FMT) matches with 75.00% similarity) + H2O = carbamoyl phosphate + L-glutamate + 2 × ADP + phosphate + 2 × H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/j.str.2013.10.016

Structure 22:185-198 (2014)

PubMed id: 24332717

Structure, functional characterization, and evolution of the dihydroorotase domain of human CAD.

A.Grande-García, N.Lallous, C.Díaz-Tejada, S.Ramón-Maiques.

ABSTRACT

Upregulation of CAD, the multifunctional protein that initiates and controls the de novo biosynthesis of pyrimidines in animals, is essential for cell proliferation. Deciphering the architecture and functioning of CAD is of interest for its potential usage as an antitumoral target. However, there is no detailed structural information about CAD other than that it self-assembles into hexamers of ∼1.5 MDa. Here we report the crystal structure and functional characterization of the dihydroorotase domain of human CAD. Contradicting all assumptions, the structure reveals an active site enclosed by a flexible loop with two Zn(2+) ions bridged by a carboxylated lysine and a third Zn coordinating a rare histidinate ion. Site-directed mutagenesis and functional assays prove the involvement of the Zn and flexible loop in catalysis. Comparison with homologous bacterial enzymes supports a reclassification of the DHOase family and provides strong evidence against current models of the architecture of CAD.