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PDBsum entry 1jdb

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Ligase PDB id
1jdb
Jmol
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

References listed in PDB file
Key reference
Title The structure of carbamoyl phosphate synthetase determined to 2.1 a resolution.
Authors J.B.Thoden, F.M.Raushel, M.M.Benning, I.Rayment, H.M.Holden.
Ref. Acta Crystallogr D Biol Crystallogr, 1999, 55, 8. [DOI no: 10.1107/S0907444998006234]
PubMed id 10089390
Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 82%.
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.
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.
Secondary reference #1
Title Structure of carbamoyl phosphate synthetase: a journey of 96 a from substrate to product.
Authors J.B.Thoden, H.M.Holden, G.Wesenberg, F.M.Raushel, I.Rayment.
Ref. Biochemistry, 1997, 36, 6305-6316. [DOI no: 10.1021/bi970503q]
PubMed id 9174345
Full text Abstract
PROCHECK
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