7QSW

L8S8-complex forming RubisCO derived from ancestral sequence reconstruction of the last common ancestor of SSU-bearing Form I RubisCOs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Evolution of increased complexity and specificity at the dawn of form I Rubiscos.

Schulz, L.Guo, Z.Zarzycki, J.Steinchen, W.Schuller, J.M.Heimerl, T.Prinz, S.Mueller-Cajar, O.Erb, T.J.Hochberg, G.K.A.

(2022) Science 378: 155-160

  • DOI: https://doi.org/10.1126/science.abq1416
  • Primary Citation of Related Structures:  
    7QSV, 7QSW, 7QSX, 7QSY, 7QSZ, 7QT1, 7QVI

  • PubMed Abstract: 

    The evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that discriminate strongly between their substrate carbon dioxide and the undesired side substrate dioxygen was an important event for photosynthetic organisms adapting to an oxygenated environment. We use ancestral sequence reconstruction to recapitulate this event. We show that Rubisco increased its specificity and carboxylation efficiency through the gain of an accessory subunit before atmospheric oxygen was present. Using structural and biochemical approaches, we retrace how this subunit was gained and became essential. Our work illuminates the emergence of an adaptation to rising ambient oxygen levels, provides a template for investigating the function of interactions that have remained elusive because of their essentiality, and sheds light on the determinants of specificity in Rubisco.


  • Organizational Affiliation

    Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RubisCO large subunit
A, C, E, G
476synthetic constructMutation(s): 0 
EC: 4.1.1.39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RubisCO small subunit
B, D, F, H
105synthetic constructMutation(s): 0 
EC: 4.1.1.39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, C, E, G
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.141 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.873α = 90
b = 131.873β = 90
c = 305.463γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description