PDBsum entry: 1xrf

Hydrolase

PDB id: 1xrf

Contents

Protein chain

363 a.a. *

Ligands

SO4

Metals

_ZN

Waters ×411

* Residue conservation analysis

PDB id:

1xrf

Name:

Hydrolase

Title:

The crystal structure of a novel, latent dihydroorotase from aeolicus at 1.7 a resolution

Structure:

Dihydroorotase. Chain: a. Synonym: dhoase. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: pyrc. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.65Å R-factor: 0.179 R-free: 0.213

Authors:

P.D.Martin,C.Purcarea,P.Zhang,A.Vaishnav,S.Sadecki,H.I.Guy-E D.R.Evans,B.F.Edwards

Key ref:

P.D.Martin et al. (2005). The crystal structure of a novel, latent dihydroorotase from Aquifex aeolicus at 1.7A resolution. J Mol Biol, 348, 535-547. PubMed id: 15826652 DOI: 10.1016/j.jmb.2005.03.015

Date:

14-Oct-04 Release date: 05-Jul-05

Protein chain

O66990  (PYRC_AQUAE) -  Dihydroorotase

Seq: 422 a.a.

Struc: 363 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.2.3 - Dihydroorotase.
• Pathway: Pyrimidine Biosynthesis
• Reaction: (S)-dihydroorotate + H₂O = N-carbamoyl-L-aspartate

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

 Gene Ontology (GO) functional annotation 

• Biological process: pyrimidine nucleotide biosynthetic process (1 term)
• Biochemical function: hydrolase activity (5 terms)

Added reference

DOI no: 10.1016/j.jmb.2005.03.015

J Mol Biol 348:535-547 (2005)

PubMed id: 15826652

The crystal structure of a novel, latent dihydroorotase from Aquifex aeolicus at 1.7A resolution.

P.D.Martin, C.Purcarea, P.Zhang, A.Vaishnav, S.Sadecki, H.I.Guy-Evans, D.R.Evans, B.F.Edwards.

ABSTRACT

Dihydroorotases (EC 3.5.2.3) catalyze the reversible cyclization of carbamoyl aspartate to form dihydroorotate in de novo pyrimidine biosynthesis. The X-ray structures of Aquifex aeolicus dihydroorotase in two space groups, C222(1) and C2, were determined at a resolution of 1.7A. These are the first structures of a type I dihydroorotase, a class of molecules that includes the dihydroorotase domain of mammalian CAD. The type I enzymes are more ancient and larger, at 45 kDa, than the type II enzymes exemplified by the 38 kDa Escherichia coli dihydroorotase. Both dihydroorotases are members of the metallo-dependent hydrolase superfamily, whose members have a distorted "TIM barrel" domain containing the active site. However, A.aeolicus dihydroorotase has a second, composite domain, which the E.coli enzyme lacks and has only one of the two zinc atoms present in the E.coli enzyme. A.aeolicus dihydroorotase is unique in exhibiting significant activity only when complexed with aspartate transcarbamoylase, whereas the E.coli dihydroorotase and the CAD dihydroorotase domain are active as free proteins. The latency of A.aeolicus dihydroorotase can be related to two differences between its structure and that of E.coli dihydroorotase: (1) the monoclinic structure has a novel cysteine ligand to the zinc that blocks the active site and possibly functions as a "cysteine switch"; and (2) active site residues that bind the substrate in E.coli dihydroorotase are located in disordered loops in both crystal structures of A.aeolicus dihydroorotase and may function as a disorder-to-order "entropy switch".

Selected figure(s)

Figure 1.
Figure 1. Amidohydrolase reactions. Dihydroorotase (DHO) and dihydropyrimidinase (DHP) catalyze the hydrolysis of cyclic amides in six atom rings. Hydantoinase (HYD) performs the same reaction on five atom rings. R is a variable substituent.

Figure 3.
Figure 3. Three-dimensional structure and active site of A. aeolicus DHO. (a) A ribbon drawing of Aa.DHO structure IIA showing the secondary structure of the N-terminal domain (residues 1-55; cyan), the b-barrel domain (residues 56-365; grey), and the C-terminal domain (residues 366-422; red). Zna is shown as a magenta ball. The visible residues (180-188) in flap-A are highlighted (yellow). (b) The C^a trace of Aa.DHO structure IIA is shown with that of Ec.DHO superposed in blue. The Ec.DHO residues corresponding to flaps A, B, and C in Aa.DHO are shown in dark magenta, magenta, and light magenta, respectively (FA, FB, FC). The visible residues (180-188) in flap-A of Aa.DHO are highlighted in yellow (FA). The Zna, Znb and dihydroorotate in the active site of Ec.DHO are displayed as space-filled models (blue). (c) The C^a trace of Aa.DHO is shown as for (b) but with the C^a trace of Ts.HYD superposed in green. The Ts.HYD residues corresponding to mobile flaps A, B, and C in Aa.DHO are shown in dark magenta, magenta, and light magenta, respectively. (d) The superposed zinc ligands are shown for Aa.DHO structure I (red), Aa.DHO structure IIA (grey), Ec.DHO (blue), and Ts.HYD (green). The ligand labels are for Aa.DHO. Cys181 in structure IIA is highlighted in yellow; the corresponding TsCys184 is highlighted in magenta. (e) The C^a trace of the visible residues of flap-A in structure IIA of Aa.DHO (grey) is shown relative to selected residues of the active site and to dihydroorotate (blue) in the active site of Ec.DHO (1j79, chain A). The side-chains of Asp179 and Asp183 are included with the C^a tracing to show binding in the active site and a hydrogen bond (broken line) with Glu213, respectively. The corresponding residues of flap-A in Ec.DHO and Ts.HYD are superposed in blue and green, respectively. Residue X is carboxylated lysine.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 348, 535-547) copyright 2005.

Figures were selected by an automated process.