PDBsum entry: 1os1

Lyase

PDB id: 1os1

Contents

Protein chain

537 a.a. *

Ligands

ATP

PYR

Metals

_MG

_CA

Waters ×260

* Residue conservation analysis

PDB id:

1os1

Name:

Lyase

Title:

Structure of phosphoenolpyruvate carboxykinase complexed wit ca and pyruvate.

Structure:

Phosphoenolpyruvate carboxykinase [atp]. Chain: a. Synonym: pep carboxykinase, phosphoenolpyruvate carboxylase ec: 4.1.1.49

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12

Resolution:

1.80Å R-factor: 0.200 R-free: 0.250

Authors:

A.Sudom,R.Walters,L.Pastushok,D.Goldie,L.Prasad,L.T.Delbaere

Key ref:

A.Sudom et al. (2003). Mechanisms of activation of phosphoenolpyruvate carboxykinase from Escherichia coli by Ca2+ and of desensitization by trypsin. J Bacteriol, 185, 4233-4242. PubMed id: 12837799 DOI: 10.1128/JB.185.14.4233-4242.2003

Date:

18-Mar-03 Release date: 23-Sep-03

Protein chain

P22259  (PCKA_ECOLI) -  Phosphoenolpyruvate carboxykinase [ATP]

Seq: 540 a.a.

Struc: 537 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.1.49 - Phosphoenolpyruvate carboxykinase (ATP).
• Reaction: ATP + oxaloacetate = ADP + phosphoenolpyruvate + CO₂

ATP (Bound ligand (Het Group name = ATP) corresponds exactly) + oxaloacetate (Bound ligand (Het Group name = PYR) matches with 66.67% similarity) = ADP + phosphoenolpyruvate + CO(2)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (8 terms)

reference

DOI no: 10.1128/JB.185.14.4233-4242.2003

J Bacteriol 185:4233-4242 (2003)

PubMed id: 12837799

Mechanisms of activation of phosphoenolpyruvate carboxykinase from Escherichia coli by Ca2+ and of desensitization by trypsin.

A.Sudom, R.Walters, L.Pastushok, D.Goldie, L.Prasad, L.T.Delbaere, H.Goldie.

ABSTRACT

The 1.8-A resolution structure of the ATP-Mg(2+)-Ca(2+)-pyruvate quinary complex of Escherichia coli phosphoenolpyruvate carboxykinase (PCK) is isomorphous to the published complex ATP-Mg(2+)-Mn(2+)-pyruvate-PCK, except for the Ca(2+) and Mn(2+) binding sites. Ca(2+) was formerly implicated as a possible allosteric regulator of PCK, binding at the active site and at a surface activating site (Glu508 and Glu511). This report found that Ca(2+) bound only at the active site, indicating that there is likely no surface allosteric site. (45)Ca(2+) bound to PCK with a K(d) of 85 micro M and n of 0.92. Glu508Gln Glu511Gln mutant PCK had normal activation by Ca(2+). Separate roles of Mg(2+), which binds the nucleotide, and Ca(2+), which bridges the nucleotide and the anionic substrate, are implied, and the catalytic mechanism of PCK is better explained by studies of the Ca(2+)-bound structure. Partial trypsin digestion abolishes Ca(2+) activation (desensitizes PCK). N-terminal sequencing identified sensitive sites, i.e., Arg2 and Arg396. Arg2Ser, Arg396Ser, and Arg2Ser Arg396Ser (double mutant) PCKs altered the kinetics of desensitization. C-terminal residues 397 to 540 were removed by trypsin when wild-type PCK was completely desensitized. Phe409 and Phe413 interact with residues in the Ca(2+) binding site, probably stabilizing the C terminus. Phe409Ala, DeltaPhe409, Phe413Ala, Delta397-521 (deletion of residues 397 to 521), Arg396(TAA) (stop codon), and Asp269Glu (Ca(2+) site) mutations failed to desensitize PCK and, with the exception of Phe409Ala, appeared to have defects in the synthesis or assembly of PCK, suggesting that the structure of the C-terminal domain is important in these processes.