5NV3 image
Deposition Date 2017-05-03
Release Date 2017-07-26
Last Version Date 2025-04-09
Entry Detail
PDB ID:
5NV3
Keywords:
LYASE
Title:
Structure of Rubisco from Rhodobacter sphaeroides in complex with CABP
Biological Source:
Source Organism:
Rhodobacter sphaeroides (Taxon ID: 1063)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.39 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5NV3 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribulose bisphosphate carboxylase large chain
Gene (Uniprot):cbbL
Chain IDs:A, C (auth: B), E (auth: C), G (auth: D), I (auth: E), K (auth: F), M (auth: G), O (auth: H)
Chain Length:467
Number of Molecules:8
Biological Source:Rhodobacter sphaeroides
UniProt ID:P27997 Pfam ID:PF02788, PF00016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribulose bisphosphate carboxylase small chain 1
Gene (Uniprot):cbbS
Chain IDs:B (auth: I), D (auth: J), F (auth: K), H (auth: L), J (auth: M), L (auth: N), N (auth: O), P
Chain Length:129
Number of Molecules:8
Biological Source:Rhodobacter sphaeroides
UniProt ID:P27998 Pfam ID:PF00101
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
KCX A LYS modified residue
Ligand Molecules
CAP
MG
Primary Citation
Mechanism of Enzyme Repair by the AAA(+) Chaperone Rubisco Activase.
Mol. Cell 67 744 756.e6 (2017)
PMID: 28803776 DOI: 10.1016/j.molcel.2017.07.004

Abstact

How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco. Hydrogen/deuterium exchange and chemical crosslinking showed that Rca structurally destabilizes elements of the Rubisco active site with remarkable selectivity. Cryo-electron microscopy revealed that Rca docks onto Rubisco over one active site at a time, positioning the C-terminal strand of RbcL, which stabilizes the catalytic center, for access to the Rca hexamer pore. The pulling force of Rca is fine-tuned to avoid global destabilization and allow for precise enzyme repair.

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Primary Citation of related structures
5NV3