1IR1

Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate

Replaces:  1BUR

Summary for 1IR1

• Entry DOI: 10.2210/pdb1ir1/pdb
• Related: 1IR2
• Descriptor: Large subunit of Rubisco, Small subunit of Rubisco, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: alpha/beta barrel, lyase
• Biological source: Spinacia oleracea (spinach); More
• Cellular location: Plastid, chloroplast: P00875 Q43832
• Total number of polymer chains: 8
• Total formula weight: 271671.48

Authors

Mizohata, E.,Matsumura, H.,Okano, Y.,Kumei, M.,Takuma, H.,Onodera, J.,Kato, K.,Shibata, N.,Inoue, T.,Yokota, A.,Kai, Y. (deposition date: 2001-08-31, release date: 2002-03-13, Last modification date: 2023-11-15)

Primary citation

Mizohata, E.,Matsumura, H.,Okano, Y.,Kumei, M.,Takuma, H.,Onodera, J.,Kato, K.,Shibata, N.,Inoue, T.,Yokota, A.,Kai, Y.
Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate.
J.Mol.Biol., 316:679-691, 2002

PubMed Abstract: Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyzes the initial steps of photosynthetic carbon reduction and photorespiratory carbon oxidation cycles by combining CO(2) and O(2), respectively, with ribulose-1,5-bisphosphate. Many photosynthetic organisms have form I rubiscos comprised of eight large (L) and eight small (S) subunits. The crystal structure of the complex of activated rubisco from the green alga Chlamydomonas reinhardtii and the reaction intermediate analogue 2-carboxyarabinitol-1,5-bisphosphate (2-CABP) has been solved at 1.84 A resolution (R(cryst) of 15.2 % and R(free) of 18.1 %). The subunit arrangement of Chlamydomonas rubisco is the same as those of the previously solved form I rubiscos. Especially, the present structure is very similar to the activated spinach structure complexed with 2-CABP in the L-subunit folding and active-site conformation, but differs in S-subunit folding. The central insertion of the Chlamydomonas S-subunit forms the longer betaA-betaB loop that protrudes deeper into the solvent channel of rubisco than higher plant, cyanobacterial, and red algal (red-like) betaA-betaB loops. The C-terminal extension of the Chlamydomonas S-subunit does not protrude into the solvent channel, unlike that of the red algal S-subunit, but lies on the protein surface anchored by interactions with the N-terminal region of the S-subunit. Further, the present high-resolution structure has revealed novel post-translational modifications. Residue 1 of the S-subunit is N(alpha)-methylmethionine, residues 104 and 151 of the L-subunit are 4-hydroxyproline, and residues 256 and 369 of the L-subunit are S(gamma)-methylcysteine. Furthermore, the unusual electron density of residue 471 of the L-subunit, which has been deduced to be threonine from the genomic DNA sequence, suggests that the residue is isoleucine produced by RNA editing or O(gamma)-methylthreonine.

PubMed: 11866526
DOI: 10.1006/jmbi.2001.5381

Experimental method

X-RAY DIFFRACTION (1.8 Å)