Table 1.
Residues comprising cores shown in Figure 2
| SCOP fold | NCBI/pfam Domains | PDB | C〈 |
Core Pos 1 |
2 | 3 | 4 | 5 | 6 | 7 | 8 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| RMSD | MSA | ||||||||||
| c51—ClassII aaRS anti-codon-binding domain | ProRS | 1nj1A | V297 | I299 | L318 | R319 | L322 | F327 | V329 | V354 | |
| cd00862: | 2.55Å | ||||||||||
| 1h4sB | |||||||||||
| 2.85Å | 17/22V | 14/22I | 6/22L | 6/22A | 19/22L | 3/22F 9I 3I 6V | 14/22V | 5/22V 6L 8I | |||
| c51—mitochondrial polymerase gamma (β) | 1g5hA | 0.4Å | V357 | L359 | L376 | L377 | L380 | I385 | V387 | V415 | |
| 1.95Å | 5/8V | 4/8L 2I | 7/8L | 1/8L | 8/8L | 4/8L | 6/8V | 4/8V | |||
| c23—flavodoxin-like | 1d5wA | 0.26Å | V6 | I8 | L19 | A20 | L23 | F28 | V30 | V52 | |
| FixJ Receiver | 2.3Å | ||||||||||
| cd00156: | 1dbwA | ||||||||||
| 1.68Å | 97/307I 95V | 144/307L | 41/307A | 237/307L | 58/307F 79Y | 184/307V | 54/307V 80I 120L | ||||
| c2—NAD(P)-binding Rossmann-fold domains | PRK06179: PRK06179 | 1jtvA | 0.44Å | V5 | I7 | L18 | A19 | L22 | F30 | V32 | V88 |
| 1.54Å | 12/24V 12A | 9/24I 15V | 1/24L | 24/24A | 14/24L 10F | 8/24 F 7Y | 24/24V | 24/24V | |||
| c3—FAD/NAD(P)-binding domain | pfam07992: | 1m6i | 0.84Å | I303 | I305 | L315 | A316 | L319 | A323 | V330 | V395 |
| Pyr_redox_2 | 1.80Å | 46/146 V 28I 24L | 53/146I 84V | 28/146L 22F 20V | 109/146A | 62/146L 32F 28A | Gapped | 117/146V | 31/146V 46L 26I | ||
| c66—SAM-dependent methyltransferases | pfam08241: Methyltransf_11 | 1r74A | 0.43Å | V60 | D62 | D70 | S71 | L74 | F79 | V81 | I136 |
| 2.55Å | 113/177D | 26/177L | 30/177A | 85/177L | 4/177F Gapped | 81/177V | 24/177V 22I 29L | ||||
| c26—adenine nucleotide α-hydrolase-like | PRK00509: PRK00509 | 1vl2A | 0.65Å | V5 | L7 | I18 | L19 | L22 | F27 | V29 | A113 |
| 2.10Å | 134/143V | 138/143L | 83/143I 43A | 51/143L 88I | 119/143L | 1/143F 18Y Gapped | 125/143V | 95/143A | |||
| c4—nucleotide-binding domain | pfam00070: Pyr_redox | 1o94A | 0.46Å | V392 | I394 | A404 | A405 | L408 | Y413 | V415 | I484 |
| 2.0Å | 37/131V | 46/131I | 25/131L 21F 7A | 102/131A | 55/131L 33F | 4/131Y 13L Gapped | 111/131V | 25/131I 46L 22V | |||
| c26—arginyl-tRNA synthetase | Class Ia aaRS | 1iq0A | 0.42Å | V105 | V107 | I132 | A133 | L136 | R141 | V143 | I350 |
| Pfam00750 | 2.3Å | 20/43V | 16/43V, 16I | 28/43I | 23/43A | 25/43L | 19/43Y 4F | 37/43V | 31/43I | ||
| c26—Tryptophanyl-tRNA synthetase | Class Ic aaRS | 1i6l | 1.83Å | I4 | F37 | (Missing) | F26 | L29 | Y33 | C35 | I140 |
| Pfam00579 | 1.72Å | (0.91Å) | (Out of order) | ||||||||
| 1mawF | |||||||||||
| 3.0Å | 19/99I 50V | 42/99F | 16/99F 47W | 46/99L | 45/99Y | 47/99C 11V | 16/99I 35L | ||||
| Structure Consensus | V | I | L | A | L | F | V | V | |||
| MSA's | V/I | I/V | I/L | A | L | F/Y | V | I/L/V |
Core residues are listed with MSA results for each domain. Structure resolutions (Å) and Cα RMSDs (Å) for core residues compared with the ProRS anti-codon-binding domain also are shown. In boldface are consensus homologs from the Class I aminoacyl-tRNA synthetase family. ArgRS is identified in Figure 1C. TrpRS has a larger RMSD, as its C-terminal β-strand is displaced to form the tryptophan-binding site. The double line separates the variant TrpRS core from those identified in Figure 1C.