Table 2. Comparison of available L8S8 Rubisco structures.
A pairwise evaluation of the sequence and structural homology between A. thaliana Rubisco and all L8S8 Rubiscos with known crystal structures. Structural superpositions were performed with PDB entries 5iu0 (A. thaliana; this work), 4hhh (Pisum sativum; Loewen et al., 2013 ▸), 4rub (Nicotiana tabacum; Suh et al., 1987 ▸), 1wdd (Oryza sativa; Matsumura et al., 2012 ▸), 8ruc (Spinacia oleracea; Andersson, 1996 ▸), 1gk8 (Chlamydomonas reinhardtii; Taylor et al., 2001 ▸), 3zxw (Thermosynechococcus elongatus; B. Terlecka, V, Wilhelmi, W. Bialek, B. Gubernator, A. Szczepania & E. Hofmann, unpublished work), 1rbl (Synechococcus sp. 6301; Newman et al., 1993 ▸), 1svd (Halothiobacillus neapolitanus; C. A. Kerfeld, M. R. Sawaya, I. Pashkov, G. Cannon, E. Williams, K. Tran & T. O. Yeates, unpublished work), 4f0k (Galdieria sulphuraria; Stec, 2012 ▸), 1bwv (Galdieria partita; Sugawara et al., 1999 ▸) and 1bxn (Alcaligenes eutrophus; Hansen et al., 1999 ▸), using the chains indicated in the table. The LSu and SSu A. thaliana sequences used for sequence comparisons were NP_051067.1 and BAB09355.1 (Rbcs1B), respectively. Unless otherwise indicated, all structures included in the comparison are of the activated Rubisco complex with 2-CABP bound.
| Chain ID | Sequence similarity to A. thaliana Rubisco | LSu | SSu | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Organism | Lineage | Rubisco form | PDB code | LSu | SSu | LSu (%) | SSu (%) | No. of aligned residues | R.m.s.d. (Å) | No. of aligned residues | R.m.s.d. (Å) |
| Pea† | Higher plant | 1B | 4hhh | A | S | 95 | 75 | 456 | 0.43 | 122 | 0.54 |
| Tobacco | Higher plant | 1B | 4rub | A | S | 94 | 74 | 460 | 0.38 | 121 | 0.48 |
| Rice | Higher plant | 1B | 1wdd | A | S | 94 | 72 | 463 | 0.25 | 122 | 1.20 |
| Spinach | Higher plant | 1B | 8ruc | A | I | 93 | 76 | 463 | 0.30 | 121 | 0.53 |
| Chlamydomonas | Green alga | 1B | 1gk8 | A | I | 88 | 49 | 463 | 0.33 | 119 | 0.88 |
| T. elongatus | Cyanobacterium | 1B | 3zxw | A | B | 82 | 46 | 462 | 0.39 | 93 | 0.79 |
| Synechococcus sp. 6301 | Cyanobacterium | 1B | 1rbl | A | I | 82 | 43 | 463 | 0.34 | 108 | 0.85 |
| H. neapolitanus ‡ | Proteobacterium | 1A | 1svd | A | M | 75 | 30 | 435 | 0.77 | 106 | 1.13 |
| G. partita | Non-green alga | 1D | 1bwv | A | S | 59 | 34 | 463 | 0.72 | 100 | 1.32 |
| G. sulphuraria ‡ | Non-green alga | 1D | 4f0k | A | B | 59 | 34 | 432 | 1.10 | 100 | 1.39 |
| A. eutrophus ‡ | Proteobacterium | 1C | 1bxn | A | I | 59 | 31 | 441 | 0.95 | 97 | 1.22 |
Activated complex with RuBP.
Non-activated complex.