6HBC

Structure of the repeat unit in the network formed by CcmM and Rubisco from Synechococcus elongatus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Rubisco condensate formation by CcmM in beta-carboxysome biogenesis.

Wang, H.Yan, X.Aigner, H.Bracher, A.Nguyen, N.D.Hee, W.Y.Long, B.M.Price, G.D.Hartl, F.U.Hayer-Hartl, M.

(2019) Nature 566: 131-135

  • DOI: 10.1038/s41586-019-0880-5
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cells use compartmentalization of enzymes as a strategy to regulate metabolic pathways and increase their efficiency 1 . The α- and β-carboxysomes of cyanobacteria contain ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)-a complex ...

    Cells use compartmentalization of enzymes as a strategy to regulate metabolic pathways and increase their efficiency 1 . The α- and β-carboxysomes of cyanobacteria contain ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)-a complex of eight large (RbcL) and eight small (RbcS) subunits-and carbonic anhydrase 2-4 . As HCO 3 - can diffuse through the proteinaceous carboxysome shell but CO 2 cannot 5 , carbonic anhydrase generates high concentrations of CO 2 for carbon fixation by Rubisco 6 . The shell also prevents access to reducing agents, generating an oxidizing environment 7-9 . The formation of β-carboxysomes involves the aggregation of Rubisco by the protein CcmM 10 , which exists in two forms: full-length CcmM (M58 in Synechococcus elongatus PCC7942), which contains a carbonic anhydrase-like domain 8 followed by three Rubisco small subunit-like (SSUL) modules connected by flexible linkers; and M35, which lacks the carbonic anhydrase-like domain 11 . It has long been speculated that the SSUL modules interact with Rubisco by replacing RbcS 2-4 . Here we have reconstituted the Rubisco-CcmM complex and solved its structure. Contrary to expectation, the SSUL modules do not replace RbcS, but bind close to the equatorial region of Rubisco between RbcL dimers, linking Rubisco molecules and inducing phase separation into a liquid-like matrix. Disulfide bond formation in SSUL increases the network flexibility and is required for carboxysome function in vivo. Notably, the formation of the liquid-like condensate of Rubisco is mediated by dynamic interactions with the SSUL domains, rather than by low-complexity sequences, which typically mediate liquid-liquid phase separation in eukaryotes 12,13 . Indeed, within the pyrenoids of eukaryotic algae, the functional homologues of carboxysomes, Rubisco adopts a liquid-like state by interacting with the intrinsically disordered protein EPYC1 14 . Understanding carboxysome biogenesis will be important for efforts to engineer CO 2 -concentrating mechanisms in plants 15-19 .


    Organizational Affiliation

    Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany. mhartl@biochem.mpg.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbon dioxide concentrating mechanism protein CcmMA92Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: ccmMSynpcc7942_1423
Find proteins for Q03513 (Synechococcus elongatus (strain PCC 7942 / FACHB-805))
Explore Q03513 
Go to UniProtKB:  Q03513
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribulose bisphosphate carboxylase large chainB, C472Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: cbbLrbcLSynpcc7942_1426
EC: 4.1.1.39
Find proteins for Q31NB3 (Synechococcus elongatus (strain PCC 7942 / FACHB-805))
Explore Q31NB3 
Go to UniProtKB:  Q31NB3
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribulose 1,5-bisphosphate carboxylase small subunitD, E111Synechococcus elongatus PCC 7942 = FACHB-805Mutation(s): 0 
Gene Names: Synpcc7942_1427
EC: 4.1.1.39
Find proteins for Q31NB2 (Synechococcus elongatus (strain PCC 7942 / FACHB-805))
Explore Q31NB2 
Go to UniProtKB:  Q31NB2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Data collection, Database references