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PDBsum entry 1ir2

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Lyase PDB id
1ir2
Jmol
Contents
Protein chains
(+ 10 more) 468 a.a. *
(+ 10 more) 140 a.a. *
Ligands
CAP ×16
GOL ×40
Metals
_MG ×16
Waters ×9999
* Residue conservation analysis

References listed in PDB file
Key reference
Title Crystal structure of activated ribulose-1,5-Bisphosphate carboxylase/oxygenase from green alga chlamydomonas reinhardtii complexed with 2-Carboxyarabinitol-1,5-Bisphosphate.
Authors E.Mizohata, H.Matsumura, Y.Okano, M.Kumei, H.Takuma, J.Onodera, K.Kato, N.Shibata, T.Inoue, A.Yokota, Y.Kai.
Ref. J Mol Biol, 2002, 316, 679-691. [DOI no: 10.1006/jmbi.2001.5381]
PubMed id 11866526
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.
Figure 2.
Figure 2. Electron-density map (2F[o] -F[c], contoured at 1s) at the active site in the Chlamydomonas L-subunit. In the stick model, C, N, O, and P atoms are colored in yellow, blue, red, and orange, respectively. 2-CABP, Mg2+, and active-site residues including carbamate LysL-201 (KcxL-201) are clearly seen in the map. The Figure was prepared using the program TURBO-FRODO.
Figure 8.
Figure 8. The omit maps (F[o] -F[c], contoured at 3.5s) of unusual residues of Chlamydomonas rubisco. Each map is calculated without a contribution of the coordinates of the unusual residue. In the stick model, C, N, O, and S atoms are colored in yellow, blue, red, and green, respectively. The stick models fitted in the electron-density maps are (a) Na-methyl-MetS-1, (b) 4-hydroxy-ProL-104, (c) 4-hydroxy-ProL-151, (d) Sg-methyl-CysL-256, (e) Sg-methyl-CysL-369, and (f) ThrL-471. The electron-density map in (f) is probably that of Og-methyl-Thr or Ile, as described in the text. The white arrows show the additional electron densities resulting from modifications or amino acid conversion. The Figure was prepared using the program TURBO-FRODO.
The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 316, 679-691) copyright 2002.
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