4F0M

UNACTIVATED RUBISCO with MAGNESIUM AND A WATER MOLECULE BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural mechanism of RuBisCO activation by carbamylation of the active site lysine.

Stec, B.

(2012) Proc.Natl.Acad.Sci.USA 109: 18785-18790

  • DOI: 10.1073/pnas.1210754109
  • Primary Citation of Related Structures:  4F0H, 4F0K

  • PubMed Abstract: 
  • Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation ste ...

    Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO(2). We report two crystal structures of nitrosylated RuBisCO from the red algae Galdieria sulphuraria with O(2) and CO(2) bound at the active site. G. sulphuraria RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO(2) defines an elusive, preactivation complex that contains a metal cation Mg(2+) surrounded by three H(2)O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming.


    Organizational Affiliation

    Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA. bog.stec.2010@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribulose bisphosphate carboxylase large chain
A
493Galdieria sulphurariaGene Names: rbcL
EC: 4.1.1.39
Find proteins for P23755 (Galdieria sulphuraria)
Go to UniProtKB:  P23755
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribulose bisphosphate carboxylase small chain
B
138Galdieria sulphurariaGene Names: rbcS
EC: 4.1.1.39
Find proteins for P23756 (Galdieria sulphuraria)
Go to UniProtKB:  P23756
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SNC
Query on SNC
A
L-PEPTIDE LINKINGC3 H6 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.159 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 136.325α = 90.00
b = 136.325β = 90.00
c = 121.524γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
CrystalCleardata collection
HKL-3000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-05-04 
  • Released Date: 2012-11-14 
  • Deposition Author(s): Stec, B.

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Database references