6URA | pdb_00006ura

Crystal structure of RUBISCO from Promineofilum breve

• PDB DOI: https://doi.org/10.2210/pdb6URA/pdb

• Classification: LYASE
• Organism(s): Candidatus Promineifilum breve
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-10-23 Released: 2020-08-19 
• Deposition Author(s): Pereira, J.H., Banda, D.M., Liu, A.K., Shih, P.M., Adams, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Novel bacterial clade reveals origin of form I Rubisco.

Banda, D.M., Pereira, J.H., Liu, A.K., Orr, D.J., Hammel, M., He, C., Parry, M.A.J., Carmo-Silva, E., Adams, P.D., Banfield, J.F., Shih, P.M.

(2020) Nat Plants 6: 1158-1166

• PubMed: 32868887 
• DOI: https://doi.org/10.1038/s41477-020-00762-4
• Primary Citation Related Structures: 
  6URA


• PubMed Abstract: 
  

  Rubisco sustains the biosphere through the fixation of CO ₂ into biomass. In plants and cyanobacteria, form I Rubisco is structurally comprised of large and small subunits, whereas all other Rubisco forms lack small subunits. The rise of the form I complex through the innovation of small subunits represents a key, yet poorly understood, transition in Rubisco's evolution. Through metagenomic analyses, we discovered a previously uncharacterized clade sister to form I Rubisco that evolved without small subunits. This clade diverged before the evolution of cyanobacteria and the origin of the small subunit; thus, it provides a unique reference point to advance our understanding of form I Rubisco evolution. Structural and kinetic data presented here reveal how a proto-form I Rubisco assembled and functioned without the structural stability imparted from small subunits. Our findings provide insight into a key evolutionary transition of the most abundant enzyme on Earth and the predominant entry point for nearly all global organic carbon.

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Organizational Affiliation: 
• Department of Plant Biology, University of California, Davis, Davis, CA, USA.
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Technology Division, Joint BioEnergy Institute, Emeryville, CA, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Lancaster Environment Centre, Lancaster University, Lancaster, UK.
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. [e-mail].
Chan Zuckerberg Biohub, San Francisco, CA, USA. [e-mail].
Department of Plant Biology, University of California, Davis, Davis, CA, USA. [e-mail].
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA. [e-mail].
Genome Center, University of California, Davis, Davis, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 206.45 kDa 
• Atom Count: 14,911 
• Modeled Residue Count: 1,762 
• Deposited Residue Count: 1,852 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase large chain	A, B, C, D	463	Candidatus Promineifilum breve	Mutation(s): 0  Gene Names: cbbL, CFX0092_B0544 EC: 4.1.1.39
UniProt
Find proteins for A0A160T9D2 (Candidatus Promineifilum breve) Explore A0A160T9D2  Go to UniProtKB:  A0A160T9D2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAP	E [auth A], G [auth B], I [auth C], K [auth D]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C6 H14 O13 P2 ITHCSGCUQDMYAI-ZMIZWQJLSA-N
MG	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.06	α = 90
b = 162.74	β = 109.57
c = 90	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Pereira, J.H., Banda, D.M., Liu, A.K., Shih, P.M., Adams, P.D.

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2020-09-16
  Changes: Database references
• Version 1.2: 2020-09-23
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection