PROSITE documentation PDOC51198

UvrD-like DNA 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 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.

Last update:

June 2006 / First entry.

Technical section

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

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

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


References

1AuthorsGorbalenya A.E., and Koonin E.V. .
TitleHelicases: amino acid sequence comparisons and structure-function relationships.
SourceCurr. Opin. Struct. Biol. 3:419-429(1993).

2AuthorsGorbalenya A.E., Koonin E.V., Donchenko A.P., Blinov V.M.
TitleTwo related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes.
SourceNucleic Acids Res. 17:4713-4730(1989).
PubMed ID2546125

3AuthorsSoultanas P., Wigley D.B.
TitleDNA helicases: 'inching forward'.
SourceCurr. Opin. Struct. Biol. 10:124-128(2000).
PubMed ID10679457

4AuthorsKorolev S., Hsieh J., Gauss G.H., Lohman T.M., Waksman G.
TitleMajor domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP.
SourceCell 90:635-647(1997).
PubMed ID9288744

5AuthorsVelankar S.S., Soultanas P., Dillingham M.S., Subramanya H.S., Wigley D.B.
TitleCrystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism.
SourceCell 97:75-84(1999).
PubMed ID10199404

6AuthorsSingleton M.R., Dillingham M.S., Gaudier M., Kowalczykowski S.C., Wigley D.B.
TitleCrystal structure of RecBCD enzyme reveals a machine for processing DNA breaks.
SourceNature 432:187-193(2004).
PubMed ID15538360
DOI10.1038/nature02988



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