SMART: Pfam domain UvrD-helicase

The domain within your query sequence starts at position 626 and ends at position 692; the E-value for the UvrD-helicase domain shown below is 8e-10.

YLKLWQLSKPLLASFDAIFVDEAQDCTPAIMNIVLSQPCGKIFVGDPHQQIYTFRGAVNA
LFTVPHT

UvrD-helicase

PFAM accession number:	PF00580
Interpro abstract (IPR034739):	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) 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 [ (PUBMED:2546125) ] 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 by a large insertion in each domain. UvrD-like DNA helicases unwind DNA with a 3'-5' polarity [ (PUBMED:10679457) ]. Crystal structures of several uvrD-like DNA helicases have been solved [ (PUBMED:9288744) (PUBMED:10199404) (PUBMED:15538360) ]. They are monomeric enzymes consisting of two domains with a common alpha-beta 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 degrees. This "domain swiveling" was proposed to be an important aspect of the mechanism of the enzyme [ (PUBMED:10199404) ]. 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'. This domain is also found in subunit AddA of bacterial helicase-nuclease complex AddAB. The AddA subunit is the one responsible for the helicase activity [ (PUBMED:21071401) ]. This entry represents the ATP-binding domain found in UvrD-like and AddA helicases.
GO function:	ATP binding (GO:0005524)

PFAM accession number:

PF00580

Interpro abstract (IPR034739):

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) 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 [ (PUBMED:2546125) ] 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 by a large insertion in each domain. UvrD-like DNA helicases unwind DNA with a 3'-5' polarity [ (PUBMED:10679457) ].

Crystal structures of several uvrD-like DNA helicases have been solved [ (PUBMED:9288744) (PUBMED:10199404) (PUBMED:15538360) ]. They are monomeric enzymes consisting of two domains with a common alpha-beta 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 degrees. This "domain swiveling" was proposed to be an important aspect of the mechanism of the enzyme [ (PUBMED:10199404) ].

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'.

This domain is also found in subunit AddA of bacterial helicase-nuclease complex AddAB. The AddA subunit is the one responsible for the helicase activity [ (PUBMED:21071401) ].

This entry represents the ATP-binding domain found in UvrD-like and AddA helicases.

GO function:

ATP binding (GO:0005524)

This is a PFAM domain. For full annotation and more information, please see the PFAM entry UvrD-helicase