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Helicases have been classified in 5 superfamilies (SF1-SF5) . 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 . For the two largest groups, commonly
referred to as SF1 and SF2, a total of seven characteristic motifs have been
identified  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 .
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 .
Some proteins that belong to the uvrD-like DNA helicase family are listed
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
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:
Gorbalenya A.E., and Koonin E.V. .
Helicases: amino acid sequence comparisons and structure-function relationships.
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