family | representative | specificity | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
|---|
COG0566A | TrmH | tRNA:Gm18 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | - | 1 | 1 | - | 1 |
COG0566B | RlmB | 23S rRNA:Gm2251 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | - | 1 | 1 | - | 1 |
COG0566C | AviRb | 23S rRNA:Um2479 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | - | 1 | 1 | - | 1 |
COG0565 | TrmJ | tRNA:Xm32 | ? | ? | ? | 1 | 1 | 1 | 1 | - | 1 | 1 | - | 1 |
COG0219 | YibK | unknown | 1 | 1 | 1 | 1 | 1 | ? | 1 | - | 1 | 1 | - | 1 |
COG4080 | PAE3113 | unknown | ? | ? | ? | 1 | 1 | ? | - | - | - | - | - | 1 |
COG4752 | TM1570 | unknown | ? | ? | ? | 1 | 1 | ? | 1 | - | - | 1 | - | 1 |
COG1772 | PF0315 | unknown | ? | ? | ? | 1 | 5 | ? | 1 | - | - | - | - | 1 |
COG1818 | PF1925 | unknown | ? | ? | ? | 3 | 1 | ? | 1 | - | - | - | - | 1 |
COG1303 | PAB1040 | tRNA:Cm56 | ? | ? | ? | 1 | 1 | 1 | 1 | - | 1 | - | - | 1 |
COG1385 | RsmE | 16S rRNA:m3U1498 | 2 | 1 | 1 | 2 | 2 | 3 | - | - | 1 | - | - | 1 |
COG2106 | MT1 | unknown | 3 | 1 | 1 | 4 | 6 | ? | 1 | - | - | 1 | - | 1 |
COG1901 | PF1403 | unknown | ? | ? | ? | 2 | 2 | ? | - | - | - | - | - | 1 |
COG1576 | YbeA | unknown | 5 | 2 | 2 | 5 | 3 | ? | - | 1 | - | - | - | 0 |
COG1756 | Nep1p | unknown | ? | ? | ? | 6 | 7 | ? | - | - | - | - | - | 1 |
COG0336 | TrmD | tRNA:m1G37 | 4 | 2 | 2 | 7 | 3 | 2 | - | 1 | - | - | - | 0 |
COG2419 | Trm10p | tRNA:m1G9 | ? | ? | ? | 8 | 4 | 2 | - | 1 | - | - | 1 | ? |
COG2428 | Yor021c | unknown | ? | ? | ? | 9 | 4 | ? | - | - | - | - | 1 | ? |
- 1. DALI Z-score > 15 in pairwise similarities: this feature clearly distinguishes four members of the 'supercluster' (COG0566 and COG0219, state 1) from other SPOUT structures (states 2–5). 2. DALI Z-score > 11 in pairwise similarities: this feature allows to split the SPOUT structures into two groups: COG0566, COG0219, COG2106, and COG1385 (state 1) vs COG0336 and COG1576 (state 2). 3. Dimerization mode (perpendicular vs antiparallel): this feature disregards the similarity of monomers, but focuses on their mutual orientation. As discussed earlier (see Figure 2), members of COG0566, COG0219, COG2106, and COG1385 form 'perpendicular' dimers (state 1), while members of COG0336 and COG1576 form 'antiparallel' dimers (state 2). 4. HHpred P-value < 1e-4 in pairwise similarities: this feature assigns state 1 to COG0556, COG0219, COG0565, COG4080, COG1303, COG4752, and COG1772, state 2 to a pair of COG1385 and COG1901, and states 3–9 to all other COGs, regarded as 'singletons'. 5. Clustering according to CLANS: here, states were arbitrarily assigned according to the visual analysis of CLANS results (Figure 4). This grouping identifies nearly the same group of closely related families as feature 4 (with the exception of inclusion of COG1818 and removal of COG1772), but allows additions groupings, in particular COG0336 with COG1576 (state 3) and COG2419 with COG2428 (state 4). Singletons are assigned states 5–7. 6. Methylation product: assigned based on experimental data. State 1: 2'-O-ribose, state 2: m1G, state 3: m3U. 7. Active site variant I: conserved Arg or Lys in the N-terminal helix and conserved Ser or Thr in the C-terminal helix. In this manuscript we predict that these residues may be characteristic for 2'-O-ribose MTases. 8. Active site variant II: conserved Arg or Lys in the C-terminal helix. This feature may be correlated with the antiparallel dimerization mode (feature 3), which requires 'migration' of the basic residue in one subunit of the dimer (compared to the 'perpendicular' mode of dimerization) to maintain the interaction with the rest of the active site in the other subunit. 9. Conserved Glu in the cofactor/methionine-binding loop: the functional significance of this conservation is unclear; this residue forms an intramolecular salt bridge and seems more important for the structural stability than for catalysis. 10. Insertion (> = 4aa) in a loop that binds adenosine of AdoMet. 11. Insertion (> = 4aa) in a loop that binds methionine of AdoMet. 12. Secondary structure of the variable Rossmanoidal part of the SPOUT fold: state 1:β-strands, state 0: 2 β-strands.
