{PDOC51198}
{PS51198; UVRD_HELICASE_ATP_BIND}
{PS51217; UVRD_HELICASE_CTER}
{BEGIN}
******************************************
* UvrD-like DNA helicase domain profiles *
******************************************

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  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°.  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.

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

-Sequences known to belong to this class detected by the second profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: June 2006 / First entry.

[ 1] Gorbalenya A.E., and Koonin E.V. .
     "Helicases: amino acid sequence comparisons and structure-function
     relationships."
     Curr. Opin. Struct. Biol. 3:419-429(1993).
[ 2] Gorbalenya A.E., Koonin E.V., Donchenko A.P., Blinov V.M.
     "Two related superfamilies of putative helicases involved in
     replication, recombination, repair and expression of DNA and RNA
     genomes."
     Nucleic Acids Res. 17:4713-4730(1989).
     PubMed=2546125
[ 3] Soultanas P., Wigley D.B.
     "DNA helicases: 'inching forward'."
     Curr. Opin. Struct. Biol. 10:124-128(2000).
     PubMed=10679457
[ 4] Korolev S., Hsieh J., Gauss G.H., Lohman T.M., Waksman G.
     "Major domain swiveling revealed by the crystal structures of
     complexes of E. coli Rep helicase bound to single-stranded DNA and
     ADP."
     Cell 90:635-647(1997).
     PubMed=9288744
[ 5] Velankar S.S., Soultanas P., Dillingham M.S., Subramanya H.S.,
     Wigley D.B.
     "Crystal structures of complexes of PcrA DNA helicase with a DNA
     substrate indicate an inchworm mechanism."
     Cell 97:75-84(1999).
     PubMed=10199404
[ 6] Singleton M.R., Dillingham M.S., Gaudier M., Kowalczykowski S.C.,
     Wigley D.B.
     "Crystal structure of RecBCD enzyme reveals a machine for processing
     DNA breaks."
     Nature 432:187-193(2004).
     PubMed=15538360; DOI=10.1038/nature02988

--------------------------------------------------------------------------------
PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and
distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives
(CC BY-NC-ND 4.0) License, see https://prosite.expasy.org/prosite_license.html
--------------------------------------------------------------------------------

{END}