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PMID:10029528

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Citation

Thoden, JB, Wesenberg, G, Raushel, FM and Holden, HM (1999) Carbamoyl phosphate synthetase: closure of the B-domain as a result of nucleotide binding. Biochemistry 38:2347-57

Abstract

Carbamoyl phosphate synthetase (CPS) catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The catalytic mechanism of the enzyme occurs through three highly reactive intermediates: carboxyphosphate, ammonia, and carbamate. As isolated from Escherichia coli, CPS is an alpha, beta-heterodimeric protein with its three active sites separated by nearly 100 A. In addition, there are separate binding sites for the allosteric regulators, ornithine, and UMP. Given the sizable distances between the three active sites and the allosteric-binding pockets, it has been postulated that domain movements play key roles for intramolecular communication. Here we describe the structure of CPS from E. coli where, indeed, such a domain movement has occurred in response to nucleotide binding. Specifically, the protein was crystallized in the presence of a nonhydrolyzable analogue, AMPPNP, and its structure determined to 2.1 A resolution by X-ray crystallographic analysis. The B-domain of the carbamoyl phosphate synthetic component of the large subunit closes down over the active-site pocket such that some atoms move by more than 7 A relative to that observed in the original structure. The trigger for this movement resides in the hydrogen-bonding interactions between two backbone amide groups (Gly 721 and Gly 722) and the beta- and gamma-phosphate groups of the nucleotide triphosphate. Gly 721 and Gly 722 are located in a Type III' reverse turn, and this type of secondary structural motif is also observed in D-alanine:D-alanine ligase and glutathione synthetase, both of which belong to the "ATP-grasp" superfamily of proteins. Details concerning the geometries of the two active sites contained within the large subunit of CPS are described.

Links

PubMed Online version:10.1021/bi982517h

Keywords

Adenosine Diphosphate/metabolism; Adenylyl Imidodiphosphate/metabolism; Binding Sites; Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/biosynthesis; Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/chemistry; Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing)/metabolism; Crystallization; Crystallography, X-Ray; Dimerization; Escherichia coli/enzymology; Metals/chemistry; Models, Molecular; Peptide Fragments/biosynthesis; Peptide Fragments/chemistry; Peptide Fragments/metabolism; Phosphates/metabolism; Protein Conformation; Purine Nucleotides/chemistry; Purine Nucleotides/metabolism

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

ECOLI:CARB

enables

GO:0005515: protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P0A6F1

F

Seeded From UniProt

complete

ECOLI:CARA

enables

GO:0005515: protein binding

ECO:0000353: physical interaction evidence used in manual assertion

UniProtKB:P00968

F

Seeded From UniProt

complete


See also

References

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