2V69

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

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This is version 1.3 of the entry. See complete history


Literature

Structural Analysis of Altered Large-Subunit Loop-6-Carboxy-Terminus Interactions that Influence Catalytic Efficiency and Co2-O2 Specificity of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase

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

(2007) Biochemistry 46: 11080

  • DOI: 10.1021/bi701063f
  • Primary Citation of Related Structures:  
    2V6A, 2V63, 2V67, 2V68, 2V69

  • PubMed Abstract: 
  • The loop between alpha-helix 6 and beta-strand 6 in the alpha/beta-barrel of ribulose-1,5-bisphosphate carboxylase/oxygenase plays a key role in discriminating between CO2 and O2. Genetic screening in Chlamydomonas reinhardtii previously identified a loop-6 V331A substitution that decreases carboxylation and CO2/O2 specificity ...

    The loop between alpha-helix 6 and beta-strand 6 in the alpha/beta-barrel of ribulose-1,5-bisphosphate carboxylase/oxygenase plays a key role in discriminating between CO2 and O2. Genetic screening in Chlamydomonas reinhardtii previously identified a loop-6 V331A substitution that decreases carboxylation and CO2/O2 specificity. Revertant selection identified T342I and G344S substitutions that restore photosynthetic growth by increasing carboxylation and specificity of the V331A enzyme. In numerous X-ray crystal structures, loop 6 is closed or open depending on the activation state of the enzyme and the presence or absence of ligands. The carboxy terminus folds over loop 6 in the closed state. To study the molecular basis for catalysis, directed mutagenesis and chloroplast transformation were used to create T342I and G344S substitutions alone. X-ray crystal structures were then solved for the V331A, V331A/T342I, T342I, and V331A/G344S enzymes, as well as for a D473E enzyme created to assess the role of the carboxy terminus in loop-6 closure. V331A disturbs a hydrophobic pocket, abolishing several van der Waals interactions. These changes are complemented by T342I and G344S, both of which alone cause decreases in CO2/O2 specificity. In the V331A/T342I revertant enzyme, Arg339 main-chain atoms are displaced. In V331A/G344S, alpha-helix 6 is shifted. D473E causes disorder of the carboxy terminus, but loop 6 remains closed. Interactions between a transition-state analogue and several residues are altered in the mutant enzymes. However, active-site Lys334 at the apex of loop 6 has a normal conformation. A variety of subtle interactions must be responsible for catalytic efficiency and CO2/O2 specificity.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAINA, B, C, D, E, F, G, H475Chlamydomonas reinhardtiiMutation(s): 1 
Gene Names: rbcL
EC: 4.1.1.39
UniProt
Find proteins for P00877 (Chlamydomonas reinhardtii)
Explore P00877 
Go to UniProtKB:  P00877
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1I, J, K, L, M, N, O, P140Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: RBCS-1CHLRE_02g120100v5CHLREDRAFT_82986
EC: 4.1.1.39
UniProt
Find proteins for P00873 (Chlamydomonas reinhardtii)
Explore P00873 
Go to UniProtKB:  P00873
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAP (Subject of Investigation/LOI)
Query on CAP

Download Ideal Coordinates CCD File 
AA [auth C], FA [auth D], KA [auth E], QA [auth F], R [auth A], UA [auth G], W [auth B], ZA [auth H]2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth H] , BA [auth C] , BB [auth H] , CA [auth C] , CB [auth H] , DA [auth C] , DB [auth H] , GA [auth D] , 
AB [auth H],  BA [auth C],  BB [auth H],  CA [auth C],  CB [auth H],  DA [auth C],  DB [auth H],  GA [auth D],  HA [auth D],  IA [auth D],  LA [auth E],  MA [auth E],  NA [auth E],  OA [auth E],  RA [auth F],  S [auth A],  SA [auth F],  T [auth A],  U [auth A],  VA [auth G],  WA [auth G],  X [auth B],  XA [auth G],  Y [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth D], JA [auth E], PA [auth F], Q [auth A], TA [auth G], V [auth B], YA [auth H], Z [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
HYP
Query on HYP
A, B, C, D, E, F, G, HL-PEPTIDE LINKINGC5 H9 N O3PRO
KCX
Query on KCX
A, B, C, D, E, F, G, HL-PEPTIDE LINKINGC7 H14 N2 O4LYS
SMC
Query on SMC
A, B, C, D, E, F, G, HL-PEPTIDE LINKINGC4 H9 N O2 SCYS
MME
Query on MME
I, J, K, L, M, N, O, PL-PEPTIDE LINKINGC6 H13 N O2 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.242α = 90
b = 169.14β = 96.24
c = 137.179γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-31
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Data collection