2OLQ

How Does an Enzyme Recognize CO2?


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

How does an enzyme recognize CO2?

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

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

  • DOI: 10.1016/j.biocel.2007.03.015
  • Primary Citation of Related Structures:  2OLR

  • PubMed 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 velociti ...

    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.


    Organizational Affiliation

    Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Sask., Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoenolpyruvate carboxykinase
A
540Escherichia coli (strain K12)Gene Names: pckA (pck)
EC: 4.1.1.49
Find proteins for P22259 (Escherichia coli (strain K12))
Go to UniProtKB:  P22259
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MN
Query on MN

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Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CO2
Query on CO2

Download SDF File 
Download CCD File 
A
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.584α = 90.00
b = 91.369β = 96.22
c = 46.577γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data reduction
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-10-18
    Type: Refinement description