Table 1.
Secondary structure features of major β-GF structural categories.
| Higher-order Classification | Representative lineages | Secondary Structural Features Common to the β-GF Fold1 | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| S1 | L1 | S2 | L2 | H | L3/LS | S3 | L4 | S4 | L5/CA | S5 | tail | notes | ||
| Basal 4-stranded versions of the β-GF | IF3-N | S1 | -- | S2 | -- | H | -- | S3 | -- | O | O | S5 | -- | |
| Archaeo-eukaryotic RNA poly. β-subunit | S1 | -- | S2 | -- | H | -- | S3 | -- | O | O | S5 | -- | ||
| Yml108w | S1 | cc | S2 | -- | H | -- | S3 | -- | O | O | S5 | h | ||
| BofC | S1 | -- | S2 | -- | H | -- | S3 | -- | O | O | S5 | -- | ||
| Immunoglobulin-binding | S1 | -- | S2 | -- | H | -- | S3 | -- | O | O | S5 | -- | ||
| POZ | S1 | -- | S2 | -- | H | h | S3 | -- | O | O | S5 | -- | ||
|
| ||||||||||||||
| Nudix superfamily | Nudix (MutT) | S1 | -- | S(ee)2 | -- | H | * | S3 | -- | O | O | S5 | e | |
|
| ||||||||||||||
| Fasciclin-like assemblage | L25 | S1 | -- | S2 | -- | H | ee* | S3 | -- | O | O | S5 | -- | 3 |
| glutamine synthetase N-terminal | S1 | -- | S2 | -- | H | eee* | S3 | -- | O | O | S5 | -- | 3 | |
| fasciclin | S1 | hhh | S2 | -- | H | ee* | S3 | -- | O | O | S5 | -- | 3 | |
| phosphoribosyl AMP cyclohydrolase (HisI) | S1 | -- | S2 | -- | H | ee* | S3 | -- | O | O | S5 | -- | 3,4 | |
|
| ||||||||||||||
| 5-stranded assemblage: classical 5-stranded clade | MoaD | S1 | H | S2 | -- | H | h** | S3 | -- | S4 | * | S5 | -- | |
| ThiS | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | * | S5 | -- | ||
| TmoB | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | * | S5 | -- | ||
| PHH-γ subunit | S1 | -- | S2 | e | H | h* | S3 | -- | S4 | e* | S5 | -- | ||
| Superantigen | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | h* | S5 | -- | ||
| Strepto/Staphylokinase | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | * | S5 | -- | ||
| YukD | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | * | S5 | -- | ||
| TGS | S1 | -- | S2 | -- | H | h* | S3 | -- | S4 | * | S5 | -- | ||
| Aldehyde OR2 N-terminal domain | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | eh* | S5 | -- | ||
|
| ||||||||||||||
| 5-stranded assemblage: Selected UB-like clade members | classic UB-like | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | * | S5 | -- | |
| PB1 | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | h* | S5 | -- | ||
| CAD/Doublecortin (DCX) | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | [h]* | S5 | -- | 6 | |
| RA | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | h* | S5 | -- | ||
| Elongin | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | * | S5 | -- | ||
| UBX | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | * | S5 | -- | ||
| E1/UFD | O | -- | S2 | -- | H | * | S3 | -- | S4 | * | S5 | S6 | 7 | |
|
| ||||||||||||||
| 5-stranded assemblage: soluble ligand binding or metal ion chelating clade | molydopterin-dependent oxidoreductase | S1 | -- | S2 | hehee | H | * | S3 | -- | S4 | eee* | S5 | -- | |
| SLBB: Nqo1-type | S1 | -- | S2 | -- | H | * | S3 | -- | S4 | hh* | S5 | -- | 5 | |
| SLBB: transcobalamin-type | S1 | -- | S2 | -- | H | eee* | S3 | -- | S4 | * | S5 | -- | ||
| 2Fe-2S ferredoxin | S1 | -- | S2 | -- | H | cc* | S3 | -- | S4 | * | S5 | -- | ||
| L-proline DH-like OR2 N-terminal domain | S1 | -- | S2 | -- | H | ee* | S3 | -- | S4 | * | S5 | -- | ||
|
| ||||||||||||||
| Miscellaneous | WWE | S1 | -- | S2 | -- | H | e* | S3 | -- | O | O | S5 | e | 8 |
| FimD N-terminal | S1 | -- | S2 | ee | H | * | S3 | -- | O | O | S5 | -- | ||
| S4 | O | O | O | O | H | h* | S3 | -- | S4 | * | S5 | -- | ||
S: Strand, L: Loop, H: Helix, LS: Lateral Shelf, CA: Connector Arm, O: absence of given feature, --: presence of a loop feature, *: presence of LS or CA, h: insert in helical conformation, e: insert in extended conformation (strand-like), cc: long coil insert.
OR: oxidoreductase.
Versions form barrel through insertion of strands at the lateral shelf.
Barrel is less pronounced in this version, strands are inserted more upstream relative to the other 3 versions.
Two small helices are present in ascending arm.
Single helix found at ascending arm in several members.
Circular permutation results in new connections between strands; the S1 strand is found at C-terminus (See Figures 1, 2).
Additional strand at tail inserted between S1 and S5; lateral shelf forms strand that also stacks with central sheet.