PDBsum entry 7jn4

Plant protein

PDB id: 7jn4

Contents

Protein chains

(+ 2 more) 427 a.a.

(+ 2 more) 138 a.a.

Waters ×232

PDB id:

7jn4

Name:

Plant protein

Title:

Rubisco in the apo state

Structure:

Ribulose bisphosphate carboxylase large chain. Chain: a, c, e, g, i, k, m, o. Synonym: rubisco large subunit. Ribulose bisphosphate carboxylase small chain 2, chloroplastic. Chain: b, d, f, h, j, l, n, p. Synonym: rubisco small subunit 2. Ec: 4.1.1.39

Source:

Chlamydomonas reinhardtii. Organism_taxid: 3055. Organism_taxid: 3055

Authors:

D.Matthies,M.C.Jonikas,S.He

Key ref:

S.He et al. (2020). The structural basis of Rubisco phase separation in the pyrenoid. Nat Plants, 6, 1480-1490. PubMed id: 33230314 DOI: 10.1016/j.bpj.2010.10.011

Date:

03-Aug-20 Release date: 18-Nov-20

Protein chains

P00877  (RBL_CHLRE) -  Ribulose bisphosphate carboxylase large chain from Chlamydomonas reinhardtii

Seq: 475 a.a.

Struc: 427 a.a.*

Protein chains

P08475  (RBS2_CHLRE) -  Ribulose bisphosphate carboxylase small subunit, chloroplastic 2 from Chlamydomonas reinhardtii

Seq: 185 a.a.

Struc: 138 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P: E.C.4.1.1.39 - ribulose-bisphosphate carboxylase.
• Reaction: 2 (2R)-3-phosphoglycerate + 2 H⁺ = D-ribulose 1,5-bisphosphate + CO2 + H2O

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.bpj.2010.10.011

Nat Plants 6:1480-1490 (2020)

PubMed id: 33230314

The structural basis of Rubisco phase separation in the pyrenoid.

S.He, H.T.Chou, D.Matthies, T.Wunder, M.T.Meyer, N.Atkinson, A.Martinez-Sanchez, P.D.Jeffrey, S.A.Port, W.Patena, G.He, V.K.Chen, F.M.Hughson, A.J.McCormick, O.Mueller-Cajar, B.D.Engel, Z.Yu, M.C.Jonikas.

ABSTRACT

Approximately one-third of global CO₂ fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO₂-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle.