PDBsum entry: 2olr

Lyase

PDB id: 2olr

Contents

Protein chain

535 a.a. *

Ligands

CO2 ×2

ATP

Metals

_MG

_CL

Waters ×454

* Residue conservation analysis

PDB id:

2olr

Name:

Lyase

Title:

Crystal structure of escherichia coli phosphoenolpyruvate carboxykinase complexed with carbon dioxide, mg2+, atp

Structure:

Phosphoenolpyruvate carboxykinase. Chain: a. Synonym: pep carboxykinase, phosphoenolpyruvate carboxylase engineered: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. Gene: pcka, pck. Expressed in: escherichia coli k12. Expression_system_taxid: 83333.

Resolution:

1.60Å R-factor: 0.176 R-free: 0.198

Authors:

J.J.Cotelesage,L.T.Delbaere,H.Goldie,J.Puttick,B.Rajabi,B.No

Key ref:

J.J.Cotelesage et al. (2007). How does an enzyme recognize CO(2)? Int J Biochem Cell Biol, 39, 1204-1210. PubMed id: 17475535 DOI: 10.1016/j.biocel.2007.03.015

Date:

19-Jan-07 Release date: 12-Jun-07

Protein chain

P22259  (PCKA_ECOLI) -  Phosphoenolpyruvate carboxykinase [ATP]

Seq: 540 a.a.

Struc: 535 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 = ADP + phosphoenolpyruvate + CO(2) (Bound ligand (Het Group name = CO2) corresponds exactly)

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: 10.1016/j.biocel.2007.03.015

Int J Biochem Cell Biol 39:1204-1210 (2007)

PubMed id: 17475535

How does an enzyme recognize CO(2)?

J.J.Cotelesage, J.Puttick, H.Goldie, B.Rajabi, B.Novakovski, L.T.Delbaere.

ABSTRACT

Phosphoenolpyruvate carboxykinase (PCK) reversibly catalyzes the carboxylation of phosphoenolpyruvate to oxaloacetate. Carbon dioxide, and not bicarbonate ion, is the substrate utilized. Assays of the carboxylation reaction show that initial velocities are 7.6-fold higher when CO(2) is used instead of HCO(3)(-). Two Escherichia coli PCK-CO(2) crystal structures are presented here. The location of CO(2) is the same for both structures; however the orientation of CO(2) is significantly different, likely from the presence of a manganese ion in one of the structures. PCK and the other three known protein-CO(2) crystal structure complexes have been compared; all have CO(2) hydrogen bonding with a basic amino acid side chain (Arg65 or Lys213 in PCK), likely to polarize CO(2) to make the central carbon atom more electrophilic and thus more reactive. Kinetic studies found that the PCK mutant Arg65Gln increased the K(M) for substrates PEP and oxaloacetate but not for CO(2). The unchanged K(M) for CO(2) can be explained since the Arg65Gln mutant likely maintains a hydrogen bond to one of the oxygen atoms of carbon dioxide.