Home | Contact

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 have been identified [2] which are distributed over two structural domains, an N-terminal ATP-binding domain and a C-terminal domain. UvrD-like DNA helicases belong to SF1, but they differ from classical SF1/SF2 (see <PDOC51192>) by a large insertion in each domain. UvrD-like DNA helicases unwind DNA with a 3'-5' polarity [3].

Crystal structures of several uvrD-like DNA helicases have been solved (see for example <PDB:1UAA>) [4,5,6]. They are monomeric enzymes consisting of two domains with a common α-β RecA-like core. The ATP-binding site is situated in a cleft between the N-terminus of the ATP-binding domain and the beginning of the C-terminal domain. The enzyme crystallizes in two different conformations (open and closed). The conformational difference between the two forms comprises a large rotation of the end of the C-terminal domain by approximately 130°. This "domain swiveling" was proposed to be an important aspect of the mechanism of the enzyme [5].

Some proteins that belong to the uvrD-like DNA helicase family are listed below:

• Bacterial UvrD helicase. It is involved in the post-incision events of nucleotide excision repair and methyl-directed mismatch repair. It unwinds DNA duplexes with 3'-5' polarity with respect to the bound strand and initiates unwinding most effectively when a single-stranded region is present.
• Gram-positive bacterial pcrA helicase, an essential enzyme involved in DNA repair and rolling circle replication. The Staphylococcus aureus pcrA helicase has both 5'-3' and 3'-5' helicase activities.
• Bacterial rep proteins, a single-stranded DNA-dependent ATPase involved in DNA replication which can initiate unwinding at a nick in the DNA. It binds to the single-stranded DNA and acts in a progressive fashion along the DNA in the 3' to 5' direction.
• Bacterial helicase IV (helD gene product). It catalyzes the unwinding of duplex DNA in the 3'-5' direction.
• Bacterial recB protein. RecBCD is a multi-functional enzyme complex that processes DNA ends resulting from a double-strand break. RecB is a helicase with a 3'-5' directionality.
• Fungal srs2 proteins, an ATP-dependent DNA helicase involved in DNA repair. The polarity of the helicase activity was determined to be 3'-5'.

To recognize uvrD-like DNA helicases we have developed two profiles. The first one recognizes the ATP-binding domain, whereas the second one is directed against the C-terminal domain.

June 2006 / First entry.

PROSITE methods (with tools and information) covered by this documentation:

UVRD_HELICASE_ATP_BIND, PS51198; UvrD-like DNA helicase ATP-binding domain profile  (MATRIX)

Sequences known to belong to this class detected by the first profile: ALL Other sequence(s) detected in Swiss-Prot: NONE.

• Domain architecture view of Swiss-Prot proteins matching PS51198 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS51198 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS51198 • Scan Swiss-Prot/TrEMBL entries against PS51198 • view ligand binding statistics

Matching PDB structures: 1PJR 1QHG 1QHH 1UAA ... [ALL]

UVRD_HELICASE_CTER, PS51217; UvrD-like DNA helicase C-terminal domain profile  (MATRIX)

Sequences known to belong to this class detected by the second profile: ALL Other sequence(s) detected in Swiss-Prot: NONE

• Domain architecture view of Swiss-Prot proteins matching PS51217 • Retrieve an alignment of Swiss-Prot true positive hits:   Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format • Retrieve the sequence logo from the alignment • Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS51217 • Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS51217 • Scan Swiss-Prot/TrEMBL entries against PS51217 • view ligand binding statistics

Matching PDB structures: 1PJR 1QHG 1QHH 1UAA ... [ALL]

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	Soultanas P., Wigley D.B.
	Title	DNA helicases: 'inching forward'.
	Source	Curr. Opin. Struct. Biol. 10:124-128(2000).
	PubMed ID	10679457

4	Authors	Korolev S., Hsieh J., Gauss G.H., Lohman T.M., Waksman G.
	Title	Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP.
	Source	Cell 90:635-647(1997).
	PubMed ID	9288744

5	Authors	Velankar S.S., Soultanas P., Dillingham M.S., Subramanya H.S., Wigley D.B.
	Title	Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism.
	Source	Cell 97:75-84(1999).
	PubMed ID	10199404

6	Authors	Singleton M.R., Dillingham M.S., Gaudier M., Kowalczykowski S.C., Wigley D.B.
	Title	Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks.
	Source	Nature 432:187-193(2004).
	PubMed ID	15538360
	DOI	10.1038/nature02988

PROSITE is copyright. It is produced by the SIB Swiss Institute Bioinformatics. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Usage by and for commercial entities requires a license agreement. For information about the licensing scheme send an email to

Prosite License or see: prosite_license.html.


View entry in original PROSITE document format
View entry in raw text format (no links)

SIB Swiss Institute of Bioinformatics | Disclaimer