Table 1.
Mechanistic characteristics of the SF1 and SF2 families.
| Number of Proteins(a) | Nucleic Acid Preference(b) | NTP Preference(c) | Unwinding Polarity(d) | Functional Classification(e) | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| H | Y | E.c. | D | R | A | G | C | U/T | 3′ 5′ | 5′ 3′ | ||
| DEAD-box | 37 | 26 | 4 | + | + | + | + | n/a (f) | ||||
| DEAH/RHA | 15 | 7 | 2 | + | + | + | + | + | + | + | (+) (g) | SF2Aα (g) |
| NS3/NPH-II | − | − | − | + | + | + | + | + | + | + | SF2Aα | |
| Ski2-like | 7 | 5 | 2 | + | + | + | + | SF2Aα | ||||
| RIG-I-like | 5 | 1 | − | + | + | + | + | SF2Aα/β(h) | ||||
| RecQ-like | 5 | 2 | 1 | + | + | + | * (i) | SF2Aα | ||||
| RecG-like | − | − | 3 | + | + | + | SF2Aβ | |||||
| Swi/Snf | 28 | 16 | 1 | + | + | n/a | SF2β | |||||
| T1R | − | − | 3 | + | + | n/a | SF2β | |||||
| Rad3/XPD | 5 | 2 | 2 | + | + | + | SF2Bα | |||||
| UvrD/Rep | 2 | 2 | 4 | + | + | + | SF1Aα | |||||
| Pif1-like | 2 | 2 | 2 | + | + | + | SF1Bα | |||||
| Upf1-like | 11 | 5 | 2 | + | + | + | + | SF1Bα | ||||
The number of proteins in each family was determined by mining the Swissprot and the Genbank databases (for more detail, see Suppl. Fig. S1, and Tab. TS1, TS2). (H – human, Y – S.cerevisiae, E.c. – E.coli).
Nucleic acid preference indicates the ability to unwind either DNA (D) or RNA (R). In families with both DNA and RNA helicases, individual proteins mostly function either as RNA or DNA helicase. Only some viral and some Upf1-like proteins have been shown to unwind both, DNA and RNA duplexes.
NTP preference indicates the ability of family members to hydrolyze all nucleotides with similar efficiency, or to be specific for adenosine triphosphates.
The unwinding polarity indicates whether proteins from a given family require duplex substrates with a single straded overhang 3′ (3′ → 5′) or 5′ (5′ → 3′) to the duplex region.
Functional classification is assigned according to the system proposed by Wigley and co-workers [3].
DEAD-box proteins, which do not unwind duplexes with defined polarity [23,24], are not classified in this system.
Several DEAH proteins have been shown to unwind with dual polarities, although 3′ → 5′ is generally preferred.
RIG-I has been shown to perform both polar unwinding (SF2Aα) [78] and translocation on duplex RNA (SF2β) [19].
Several RecQ-like proteins are specific for distinct DNA structures, and it is not clear whether all family members display unique polarity on these substrates.