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| PROSITE documentation PDOC51192 |
Superfamilies 1 and 2 helicase domain profiles
Description
Helicases have been classified in 5 superfamilies (SF1-SF5) [1]. All of the
proteins bind ATP and, consequently, all of them carry the classical Walker A
(phosphate-binding loop or P-loop) (see <PDOC00017>) and Walker B
(Mg2+-binding aspartic acid) motifs [1]. For the two largest groups, commonly
referred to as SF1 and SF2, a total of seven characteristic motifs has been
identified [2]. These two superfamilies encompass a large number of DNA and
RNA helicases from archaea, eubacteria, eukaryotes and viruses that seem to be
active as monomers or dimers. RNA and DNA helicases are considered to be
enzymes that catalyze the separation of double-stranded nucleic acids in an
energy-dependent manner [3].
The various structures of SF1 and SF2 helicases present a common core with two
α-β RecA-like domains (see for example <PDB:1FUU>) [3,4]. The
structural homology with the RecA recombination protein covers the five
contiguous parallel β strands and the tandem α helices. ATP binds to
the amino proximal α-β domain, where the Walker A (motif I) and Walker
B (motif II) are found. The N-terminal domain also contains motif III (S-A-T)
which was proposed to participate in linking ATPase and helicase activities.
The carboxy-terminal α-β domain is structurally very similar to the
proximal one even though it is bereft of an ATP-binding site, suggesting that
it may have originally arisen through gene duplication of the first one.
Some members of helicase superfamilies 1 and 2 are listed below:
- DEAD-box RNA helicases (see <PDOC00039>). The prototype of DEAD-box
proteins is the translation initiation factor eIF4A. The eIF4A protein is
an RNA-dependent ATPase which functions together with eIF4B as an RNA
helicases [5,E1].
- DEAH-box RNA helicases (see <PDOC00039>). Mainly pre-mRNA-splicing factor
ATP-dependent RNA helicases [5,E1].
- Eukaryotic DNA repair helicase RAD3/ERCC-2, an ATP-dependent 5'-3' DNA
helicase involved in nucleotide excision repair of UV-damaged DNA.
- Eukaryotic TFIIH basal transcription factor complex helicase XPB subunit.
An ATP-dependent 3'-5' DNA helicase which is a component of the core-TFIIH
basal transcription factor, involved in nucleotide excision repair (NER) of
DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II.
It acts by opening DNA either around the RNA transcription start site or
the DNA.
- Eukaryotic ATP-dependent DNA helicase Q. A DNA helicase that may play a
role in the repair of DNA that is damaged by ultraviolet light or other
mutagens.
- Eukaryotic ATP-dependent helicase SNF2/RAD54. A group of ATP-dependent
remodelling factors frequently found associated with histone deacetylases.
- Bacterial and eukaryotic antiviral SKI2-like helicase. SKI2 has a role in
the 3'-mRNA degradation pathway. It represses dsRNA virus propagation by
specifically blocking translation of viral mRNAs, perhaps recognizing the
absence of CAP or poly(A).
- Bacterial DNA-damage-inducible protein G (DinG). A probable helicase
involved in DNA repair and perhaps also replication.
- Bacterial primosomal protein N' (PriA). PriA protein is one of seven
proteins that make up the restart primosome, an apparatus that promotes
assembly of replisomes at recombination intermediates and stalled
replication forks.
- Bacterial ATP-dependent DNA helicase recG. It has a critical role in
recombination and DNA repair. It helps process Holliday junction
intermediates to mature products by catalyzing branch migration. It has a
DNA unwinding activity characteristic of a DNA helicase with a 3' to 5'
polarity.
- ssRNA positive-strand flaviviruses and potyviruses RNA helicase.
- dsDNA viruses early transcription factor 70 kDa subunit.
- dsDNA viruses nucleoside triphosphatase I (NPH I) protein. It serves two
roles in transcription; it acts in concert with viral termination
factor/capping enzyme to catalyze release of UUUUUNU-containing nascent RNA
from the elongation complex, and it acts by itself as a polymerase
elongation factor to facilitate readthrough of intrinsic pause sites.
- Poxviruses transcript release DNA helicase. It prevents virus-induced
breakdown of RNA. It acts as a negative transcription elongation factor. It
is involved in an ATP-dependent manner in release of nascent RNA.
To recognize helicase Superfamilies 1 and 2 we have developed two profiles.
The first one recognizes all classical SF1 and SF2 helicases except bacterial
DinG protein and eukaryotic Rad3 which belong to the same subfamily and which
differ from other SF1-SF2 helicases by the presence of a large insert after
the Walker A [6]. Our second profile recognizes specifically this subfamily.
UvrD (see <PDOC51198>) also belong to SF1 but is not picked-up by these
profiles.
secA is a bacterial protein important for protein export which also
contains the seven motifs characteristic of SF1 and SF2. We also developed a
profile specific for this family (see <PDOC01016>).
April 2006 / First entry.
Technical section
PROSITE methods (with tools and information) covered by this documentation:
| HELICASE_ATP_BIND_1, PS51192; Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile (MATRIX) |
| Sequences known to belong to this class detected by the first profile: |
ALL |
| Other sequence(s) detected in Swiss-Prot: |
NONE. |
|
|
|
| Matching PDB structures:
1A1V 1C4O 1CU1 1D2M ... [ALL] |
| HELICASE_ATP_BIND_2, PS51193; Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile (MATRIX) |
| Sequences known to belong to this class detected by the second profile: |
ALL |
| Other sequence(s) detected in Swiss-Prot: |
NONE. |
|
|
|
| Matching PDB structures:
2VSF 3CRV 3CRW 4A15 [ALL] |
| HELICASE_CTER, PS51194; Superfamilies 1 and 2 helicase C-terminal domain profile (MATRIX) |
| Sequences known to belong to this class detected by the third profile: |
ALL |
| Other sequence(s) detected in Swiss-Prot: |
NONE. |
|
|
|
| Matching PDB structures:
1A1V 1C4O 1CU1 1D2M ... [ALL] |
References
| 1 |
Authors |
Gorbalenya A.E., and Koonin E.V. . |
| Title |
Helicases: amino acid sequence comparisons and structure-function relationships. |
| Source |
Curr. Opin. Struct. Biol. 3:419-429(1993). |
| 2 |
Authors |
Gorbalenya A.E., Koonin E.V., Donchenko A.P., Blinov V.M. |
| Title |
Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. |
| Source |
Nucleic Acids Res. 17:4713-4730(1989). |
| PubMed ID |
2546125 |
| 3 |
Authors |
Caruthers J.M., McKay D.B. |
| Title |
Helicase structure and mechanism. |
| Source |
Curr. Opin. Struct. Biol. 12:123-133(2002). |
| PubMed ID |
11839499 |
| 4 |
Authors |
Caruthers J.M., Johnson E.R., McKay D.B. |
| Title |
Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase. |
| Source |
Proc. Natl. Acad. Sci. U.S.A. 97:13080-13085(2000). |
| PubMed ID |
11087862 |
| DOI |
10.1073/pnas.97.24.13080 |
| 5 |
Authors |
Tanner N.K., Linder P. |
| Title |
DExD/H box RNA helicases: from generic motors to specific dissociation functions. |
| Source |
Mol. Cell 8:251-262(2001). |
| PubMed ID |
11545728 |
| 6 |
Authors |
Koonin E.V. |
| Title |
Escherichia coli dinG gene encodes a putative DNA helicase related to a group of eukaryotic helicases including Rad3 protein. |
| Source |
Nucleic Acids Res. 21:1497-1497(1993). |
| PubMed ID |
8385320 |
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