Table 1. Shared features of the SLOG superfamily.
| Secondary structure elements and conserved residue positions common to SLOG superfamily | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Higher order clade | Family name (pdbid) | S1 small residue loop | S1 loop binding pocket resi. | S2 small residue loop | H2 binding pocket residue | S3 loop residues | H3/dH3 | H4 binding pocket residue | S5 small residue loop | H5 binding pocket residues | H6/H6a-H6b; presence/absence of S7 and H7 |
| LOG proper | classic LOG (2Q4D) | GS | - | GGG | M | PxxL | dH3 | RK | PGG | TxE/DE | H6a-H6b; S7 and H7 present |
| Moco-binding (2IZ5) | GsG | - | sGG | M | P- | dH3 | R | GxG | TxxE | H6; S7 and H7 present | |
| Genome tandem LOG (1WEK) | GSs | - | GGGsG | M | PF | dH3 | RK | PGG | TxDE | H6a-H6b; S7 and H7 present | |
| DUF4478/3412 fusion (4NPA) | GG | H | GCG | M | P- | dH3 | R | PGG | TxEE | H6a-H6b; S7 and H7 present | |
| Sir2/TIR-associating | STALD (Sir2/TIR-Associating LOG-Smf/DprA) | SGs | p | sGxG | h | PF | dH3 | R | GSR/K | xxxE | H6-H6b?; cpS7 and cpH7 present |
| LDcluster2 | SxS | D | GG- | h | P- | H3 | oxMR | GG- | xxEE | H6; H7 present, S7 possibly absent | |
| LDcluster3 | SxS | R | GGH | h | Qo | dH3 | SxxxMR | GG- | xxxE | H6; H7 present, S7 possibly absent | |
| LDcluster4 | GSG | - | TGss | h | P- | dH3 | R | sG- | TxxE | H6; S7 and H7 present | |
| TPALS (TIR/PNP-Associating LOG-DprA/Smf) | GS | - | -ss | DW | polar patch | H3 | Q | GGG | —p | H6; S7 and H7 present | |
| YpsA proper | YpsA (2NX2) | oG | R | ss- | GxD/E | PF | H3 | a | D/Ns | Txxx | H6, S7, H7 absent |
| cpYpsA (3IMK) | NxAGs (cpS1,H1) | R | SGGQ | GxD | P- (dS3) | dH3 | RTxxN | — | GoxxT | H6; S7 and H7 absent | |
| YAcAr (YspA, cpYpsA related) | sGs | - | Gs | GxD/E | – | dH3 | RN | SG- | oxxx | H6, S7, H7 absent | |
| LSDAT proper | LSDAT (LOG-Smf/DprA in TRPM) prokaryote | GGA | - | ssGT | h | – | dH3 | WxxE | sGG | TxxE/D | H6a-H6b; S7 and H7 present |
| LSDAT (LOG-Smf/DprA in TRPM) eukaryote | GG | - | ssG | - | – | dH3 | ExxxR | -GG | —- | H6a-H6b; S7 and H7 present | |
| SMF/DprA | Smf/DprA (4LJR) | Gs | R | SGxA | GxD | Px[6]Y | H3 | RN/D | — | —- | ee-H6; S7 and H7 present |
Abbreviations: o, serine/threonine; s, small residue; h, long hydrophobic residue; x, any residue; d, degenerate secondary structure element; a, aromatic; ?, presence of element not clear from alignment; cp, circularly-permuted element; -, element or residue not conserved; ee, extended loop; resi, residue.