PDBsum entry 1ce8

Ligase imp

PDB id: 1ce8

Contents

Protein chains

1058 a.a. *

379 a.a. *

Ligands

PO4 ×4

ADP ×8

ORN ×8

IMP ×4

NET ×4

Metals

__K ×28

_MN ×12

_CL ×12

Waters ×4037

* Residue conservation analysis

PDB id:

1ce8

Name:

Ligase imp

Title:

Carbamoyl phosphate synthetase from escherichis coli with complexed with the allosteric ligand imp

Structure:

Protein (carbamoyl-phosphate synthase). Chain: a, c, e, g. Engineered: yes. Other_details: long chain. Protein (carbamoyl-phosphate synthase). Chain: b, d, f, h. Engineered: yes. Other_details: short chain

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Hetero-Tetramer (from PDB file)

Resolution:

2.10Å R-factor: 0.192 R-free: 0.250

Authors:

J.B.Thoden,F.M.Raushel,H.M.Holden

Key ref:

J.B.Thoden et al. (1999). The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase. J Biol Chem, 274, 22502-22507. PubMed id: 10428826 DOI: 10.1074/jbc.274.32.22502

Date:

18-Mar-99 Release date: 26-Jul-99

Protein chains

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

Seq: 1073 a.a.

Struc: 1058 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 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H: E.C.6.3.5.5 - carbamoyl-phosphate synthase (glutamine-hydrolyzing).
• Pathway: Pyrimidine Biosynthesis
• 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 = ORN) matches with 90.00% similarity) = 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)

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

reference

DOI no: 10.1074/jbc.274.32.22502

J Biol Chem 274:22502-22507 (1999)

PubMed id: 10428826

The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase.

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

ABSTRACT

Carbamoyl phosphate synthetase (CPS) from Escherichia coli catalyzes the formation of carbamoyl phosphate, which is subsequently employed in both the pyrimidine and arginine biosynthetic pathways. The reaction mechanism is known to proceed through at least three highly reactive intermediates: ammonia, carboxyphosphate, and carbamate. In keeping with the fact that the product of CPS is utilized in two competing metabolic pathways, the enzyme is highly regulated by a variety of effector molecules including potassium and ornithine, which function as activators, and UMP, which acts as an inhibitor. IMP is also known to bind to CPS but the actual effect of this ligand on the activity of the enzyme is dependent upon both temperature and assay conditions. Here we describe the three-dimensional architecture of CPS with bound IMP determined and refined to 2.1 A resolution. The nucleotide is situated at the C-terminal portion of a five-stranded parallel beta-sheet in the allosteric domain formed by Ser(937) to Lys(1073). Those amino acid side chains responsible for anchoring the nucleotide to the polypeptide chain include Lys(954), Thr(974), Thr(977), Lys(993), Asn(1015), and Thr(1017). A series of hydrogen bonds connect the IMP-binding pocket to the active site of the large subunit known to function in the phosphorylation of the unstable intermediate, carbamate. This structural analysis reveals, for the first time, the detailed manner in which CPS accommodates nucleotide monophosphate effector molecules within the allosteric domain.

Selected figure(s)

Figure 3.
Fig. 3. The IMP binding pocket. Panel a, a close-up view of those amino acid residues located within approximately 5 Å of atoms of the IMP. Panel b, a cartoon of potential hydrogen bonds between the ligand and the protein, as indicated by the dashed lines.

Figure 4.
Fig. 4. Superposition of the CPS allosteric binding pockets with bound IMP or glutamine/inorganic phosphate. The model described in this report is shown in black, whereas the structure of CPS complexed with glutamine and inorganic phosphate, as described by Thoden et al. (2), is displayed in red. Note the nearly exact correspondence between the inorganic phosphate and the phosphoryl moiety of the nucleotide.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 22502-22507) copyright 1999.

Figures were selected by an automated process.