1UWA

L290F mutant rubisco from chlamydomonas


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Altered Intersubunit Interactions in Crystal Structures of Catalytically Compromised Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase

Karkehabadi, S.Taylor, T.C.Spreitzer, R.J.Andersson, I.

(2005) Biochemistry 44: 113

  • DOI: 10.1021/bi047928e
  • Primary Citation of Related Structures:  1UW9

  • PubMed Abstract: 
  • Substitution of Leu290 by Phe (L290F) in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from the unicellular green alga Chlamydomonas reinhardtii causes a 13% decrease in CO(2)/O(2) specificity and reduced thermal stability. Gen ...

    Substitution of Leu290 by Phe (L290F) in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from the unicellular green alga Chlamydomonas reinhardtii causes a 13% decrease in CO(2)/O(2) specificity and reduced thermal stability. Genetic selection for restored photosynthesis at the restrictive temperature identified an Ala222 to Thr (A222T) substitution that suppresses the deleterious effects of the original mutant substitution to produce a revertant enzyme with improved thermal stability and kinetic properties virtually indistinguishable from that of the wild-type enzyme. Because the mutated residues are situated approximately 19 A away from the active site, they must affect the relative rates of carboxylation and oxygenation in an indirect way. As a means for elucidating the role of such distant interactions in Rubisco catalysis and stability, we have determined the crystal structures of the L290F mutant and L290F/A222T revertant enzymes to 2.30 and 2.05 A resolution, respectively. Inspection of the structures reveals that the mutant residues interact via van der Waals contacts within the same large subunit (intrasubunit path, 15.2 A Calpha-Calpha) and also via a path involving a neighboring small subunit (intersubunit path, 18.7 A Calpha-Calpha). Structural analysis of the mutant enzymes identified regions (residues 50-72 of the small subunit and residues 161-164 and 259-264 of the large subunit) that show significant and systematically increased atomic temperature factors in the L290F mutant enzyme compared to wild type. These regions coincide with residues on the interaction paths between the L290F mutant and A222T suppressor sites and could explain the temperature-conditional phenotype of the L290F mutant strain. This suggests that alterations in subunit interactions will influence protein dynamics and, thereby, affect catalysis.


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, BMC Box 590, 751 24 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
A, B, E, H, K, O, R, V
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
C, F, I, J, M, P, T, W
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, E, F, H, I, J, K, M, O, P, R, T, V
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, E, H, K, O, R, V
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CAP
Query on CAP

Download SDF File 
Download CCD File 
A, B, E, H, K, O, R, V
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B, E, H, K, O, R, V
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
SMC
Query on SMC
A, B, E, H, K, O, R, V
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
HYP
Query on HYP
A, B, E, H, K, O, R, V
L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 120.983α = 90.00
b = 177.709β = 117.70
c = 122.663γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-12
    Type: Data collection, Derived calculations