PDBsum entry 1jdb

Ligase

PDB id: 1jdb

Contents

Protein chains

1057 a.a. *

379 a.a. *

Ligands

PO4 ×9

GLN ×8

ADP ×8

ORN ×4

NET ×4

Metals

_CL ×29

_MN ×16

__K ×29

Waters ×4857

* Residue conservation analysis

PDB id:

1jdb

Name:

Ligase

Title:

Carbamoyl phosphate synthetase from escherichia coli

Structure:

Carbamoyl phosphate synthetase. Chain: b, e, h, k. Carbamoyl phosphate synthetase. Chain: c, f, i, l. Ec: 6.3.5.5

Source:

Escherichia coli. Organism_taxid: 562. Organism_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.179

Authors:

J.B.Thoden,H.M.Holden,G.Wesenberg,F.M.Raushel,I.Rayment

Key ref:

J.B.Thoden et al. (1999). The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution. Acta Crystallogr D Biol Crystallogr, 55, 8. PubMed id: 10089390 DOI: 10.1107/S0907444998006234

Date:

25-Mar-97 Release date: 17-Jun-98

Protein chains

P00968  (CARB_ECOLI) -  Carbamoyl phosphate synthase large chain from Escherichia coli (strain K12)

Seq: 1073 a.a.

Struc: 1057 a.a.

Protein chains

P0A6F1  (CARA_ECOLI) -  Carbamoyl phosphate synthase small chain from Escherichia coli (strain K12)

Seq: 382 a.a.

Struc: 379 a.a.*

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

Enzyme reactions

• Enzyme class 1: Chains B, E, H, K: E.C.6.3.4.16 - carbamoyl-phosphate synthase (ammonia).
• Pathway: Pyrimidine Biosynthesis
• Reaction: hydrogencarbonate + NH4⁺ + 2 ATP = carbamoyl phosphate + 2 ADP + phosphate + 2 H⁺

hydrogencarbonate + NH4(+) + 2 × ATP = carbamoyl phosphate (Bound ligand (Het Group name = ADP) corresponds exactly) + 2 × ADP + phosphate + 2 × H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

• Enzyme class 2: Chains B, C, E, F, H, I, K, L: 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 + H2O (Bound ligand (Het Group name = GLN) corresponds exactly) = 2 × carbamoyl phosphate (Bound ligand (Het Group name = ADP) corresponds exactly) + L-glutamate + 2 × ADP + phosphate + 2 × H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

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: 10.1107/S0907444998006234

Acta Crystallogr D Biol Crystallogr 55:8 (1999)

PubMed id: 10089390

The structure of carbamoyl phosphate synthetase determined to 2.1 A resolution.

J.B.Thoden, F.M.Raushel, M.M.Benning, I.Rayment, H.M.Holden.

ABSTRACT

Carbamoyl phosphate synthetase catalyzes the formation of carbamoyl phosphate from one molecule of bicarbonate, two molecules of Mg2+ATP and one molecule of glutamine or ammonia depending upon the particular form of the enzyme under investigation. As isolated from Escherichia coli, the enzyme is an alpha,beta-heterodimer consisting of a small subunit that hydrolyzes glutamine and a large subunit that catalyzes the two required phosphorylation events. Here the three-dimensional structure of carbamoyl phosphate synthetase from E. coli refined to 2.1 A resolution with an R factor of 17.9% is described. The small subunit is distinctly bilobal with a catalytic triad (Cys269, His353 and Glu355) situated between the two structural domains. As observed in those enzymes belonging to the alpha/beta-hydrolase family, the active-site nucleophile, Cys269, is perched at the top of a tight turn. The large subunit consists of four structural units: the carboxyphosphate synthetic component, the oligomerization domain, the carbamoyl phosphate synthetic component and the allosteric domain. Both the carboxyphosphate and carbamoyl phosphate synthetic components bind Mn2+ADP. In the carboxyphosphate synthetic component, the two observed Mn2+ ions are both octahedrally coordinated by oxygen-containing ligands and are bridged by the carboxylate side chain of Glu299. Glu215 plays a key allosteric role by coordinating to the physiologically important potassium ion and hydrogen bonding to the ribose hydroxyl groups of ADP. In the carbamoyl phosphate synthetic component, the single observed Mn2+ ion is also octahedrally coordinated by oxygen-containing ligands and Glu761 plays a similar role to that of Glu215. The carboxyphosphate and carbamoyl phosphate synthetic components, while topologically equivalent, are structurally different, as would be expected in light of their separate biochemical functions.

Selected figure(s)

Figure 7.
Figure 7 The active site for the carboxyphosphate synthetic component. A cartoon of potential hydrogen-bonding interactions between the ADP/P[i] moiety and the protein is displayed. The manganese ions are indicated as brown spheres.

Figure 13.
Figure 13 A close-up view of the ornithine binding pocket. Ordered water molecules are indicated by the red spheres. The carboxylate group of ornithine interacts with the allosteric domain while the -amino group of the side chain forms hydrogen bonds with amino-acid residues from the carbamoyl phosphate synthetic component.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1999, 55, 8-0) copyright 1999.

Figures were selected by an automated process.