|
Secondary structure features of major β-GF structural categories. |
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| Higher-order Classification |
Lineage Name |
Secondary Structural Features Common to the β-GF Fold1 |
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|
|
||||||||||||||
| S1 |
L1 |
S2 |
L2 |
H |
L3/LS |
S3 |
L4 |
S4 |
L5/CA |
S5 |
tail |
notes |
||
|
|
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| Basal 4-stranded versions of the β-GF |
IF3-N |
S1 |
-- |
S2 |
-- |
H |
-- |
S3 |
-- |
O |
O |
S5 |
-- |
|
| Archeo-eukaryotic RNA poly. β-subunit |
S1 |
-- |
S2 |
-- |
H |
-- |
S3 |
-- |
O |
O |
S5 |
-- |
||
| Sporadically-distributed 4-stranded versions |
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 |
-- |
||
| 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 eukaryote UB-like superfamily 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 |
-- |
||
|
1. 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. 2. OR: oxidoreductase. 3. Versions form barrel through insertion of strands at the lateral shelf. 4. Barrel is less pronounced in this version, strands are inserted more upstream relative to the other 3 versions. 5. Two small helices are present in ascending arm. 6. Single helix found at ascending arm in several members. 7. Circular permutation results in new connections between strands; the S1 strand is found at C-terminus (See Figures 1, 2). 8. Additional strand at tail inserted between S1 and S5; lateral shelf forms strand that also stacks with central sheet. | ||||||||||||||
Burroughs et al. Biology Direct 2007 2:18 doi:10.1186/1745-6150-2-18 |
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