2VDH

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C172S mutation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Functional Consequences of the Replacement of Proximal Residues Cys-172 and Cys-192 in the Large Subunit of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase from Chlamydomonas Reinhardtii

Garcia-Murria, M.-J.Karkehabadi, S.Marin-Navarro, J.Satagopan, S.Andersson, I.Spreitzer, R.J.Moreno, J.

(2008) Biochem.J. 411: 241

  • DOI: 10.1042/BJ20071422
  • Primary Citation of Related Structures:  2VDI

  • PubMed Abstract: 
  • Proximal Cys(172) and Cys(192) in the large subunit of the photosynthetic enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39) are evolutionarily conserved among cyanobacteria, algae and higher plants. Mutation of Cys(172) ha ...

    Proximal Cys(172) and Cys(192) in the large subunit of the photosynthetic enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39) are evolutionarily conserved among cyanobacteria, algae and higher plants. Mutation of Cys(172) has been shown to affect the redox properties of Rubisco in vitro and to delay the degradation of the enzyme in vivo under stress conditions. Here, we report the effect of the replacement of Cys(172) and Cys(192) by serine on the catalytic properties, thermostability and three-dimensional structure of Chlamydomonas reinhardtii Rubisco. The most striking effect of the C172S substitution was an 11% increase in the specificity factor when compared with the wild-type enzyme. The specificity factor of C192S Rubisco was not altered. The V(c) (V(max) for carboxylation) was similar to that of wild-type Rubisco in the case of the C172S enzyme, but approx. 30% lower for the C192S Rubisco. In contrast, the K(m) for CO(2) and O(2) was similar for C192S and wild-type enzymes, but distinctly higher (approximately double) for the C172S enzyme. C172S Rubisco showed a critical denaturation temperature approx. 2 degrees C lower than wild-type Rubisco and a distinctly higher denaturation rate at 55 degrees C, whereas C192S Rubisco was only slightly more sensitive to temperature denaturation than the wild-type enzyme. X-ray crystal structures reveal that the C172S mutation causes a shift of the main-chain backbone atoms of beta-strand 1 of the alpha/beta-barrel affecting a number of amino acid side chains. This may cause the exceptional catalytic features of C172S. In contrast, the C192S mutation does not produce similar structural perturbations.


    Organizational Affiliation

    Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Universitat de València, Av. Dr Moliner 50, Burjassot, València E-46100, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
A, B, C, D, E, F, G, H
475Chlamydomonas reinhardtiiGene Names: rbcL
EC: 4.1.1.39
Find proteins for P00877 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P00877
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1
I, J, K, L, M, N, O, P
140Chlamydomonas reinhardtiiGene Names: RBCS-1
EC: 4.1.1.39
Find proteins for P00873 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P00873
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CAP
Query on CAP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
SMC
Query on SMC
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
HYP
Query on HYP
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H9 N O3PRO
MME
Query on MME
I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC6 H13 N O2 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 120.190α = 90.00
b = 178.349β = 117.87
c = 122.561γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance