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Table 3 Twenty most often positively selected rbcL residues

From: Widespread positive selection in the photosynthetic Rubisco enzyme

Residue No 1

N 2

Location of residue

Residues within 5 Å 3

Structural motifs within 5 Å

Interactions4

251

46

helix 3

247, 248, 249, 250, 252, 253, 254, 255, 256, 279, 280, 283

helixes 3, 4

DD, SSU

225

39

helix 2

189, 190, 193, 194, 221, 222, 223, 224, 226, 227, 228, 229, 236, 237, 238

helixes 1, 2; strand 3

SSU

142

31

helix D

33, 140, 141, 143, 144, 145, 146, 367, 369

N-terminus; strands D, H

DD

328

28

loop 6

295, 311, 326, 327, 329, 330, 342, 345, 346, 349, 376, 377, 378, 394

AS; loop 6 region; helixes 5, 7; strand 7

AS

449

28

helix G

445, 446, 447, 448, 450, 451, 452, 453, 455, 456

C-terminus

SSU

145

27

helix D

140, 141, 142, 143, 144, 146, 147, 148, 320, 366, 367, 368, 369, 371

helixes D, 5, H

DD

86

23

strand C

25, 27, 84, 85, 87, 88, 98, 99, 100

strands A, C, D

RA

309

22

strand F

117, 121, 125, 134, 135, 301, 302, 307, 308, 310, 311, 313, 314

strand E; helixes F, 5

ID

95

21

 

42, 43, 44, 93, 94, 96, 97, 131

strands B, D, E

ID, RA

375

19

strand 7

155, 158, 159, 169, 324, 325, 326, 373, 374, 376, 377, 397, 398, 399

helix E; strands 6, 7, 8

SSU

470

19

C-terminus

336, 468, 469, 471, 472

loop 6; C-terminus

ID, RA

279

18

helix 4

250, 251, 274, 275, 276, 277, 278, 280, 281, 282, 283

helixes 3, 4

 

219

17

helix 2

58I, 59I, 61I, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 256, 260

helixes 2, 3

SSU, DD

255

17

helix 3

251, 252, 253, 254, 256, 257, 258, 259, 283

helixes 3, 4

SSU, DD

28

15

N-terminus

25, 26, 27, 29, 30, 84

strands A, C

 

228

14

helix 2

190, 193, 194, 224, 225, 226, 227, 229, 230, 231, 232, 236

helixes 1, 2

SSU

97

13

strand D

40, 41, 42, 44, 50, 87, 88, 89, 90, 95, 96, 98, 99, 100

helix B; strands B, C, D

RA

262

12

 

59S, 60S, 226, 240, 257, 258, 260, 261, 263, 264, 289

helixes 2, 3; strand 3

SSU, DD

439

12

helix G

436, 437, 438, 440, 441

helix G

 

282

10

helix 4

149, 278, 279, 280, 281, 283, 284, 285, 286, 321

helixes 4, 5

DD, SSU

  1. 1 Numbering of residues is after the spinach Rubisco sequence.
  2. 2 Number of groups with detected signal of positive selection where the particular residue was shown under positive selection with Bayesian posterior probability larger than 0.95, when analyzed by the Bayes Empirical Bayes [20].
  3. 3 Subscriptions denote residues from I and S small subunits. Residues within the list of the twenty designated residues are underlined.
  4. 4 Interactions in which the twenty selected residues and/or residues within 5 Å of them are involved. AS – interactions with the active site; ID – intradimer interactions; DD – dimer-dimer interactions; RA – interface for interactions with Rubisco activase; SSU – interactions with small subunits; after [8]. Interactions based on literature survey only are given in italics; after [1,23,27].
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BMC Ecology and Evolution

ISSN: 2730-7182

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