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Vol. 10, Issue 1, 5-16, January 2000
The Bacterial Replicative Helicase DnaB Evolved from a RecA Duplication
Detlef D.
Leipe,1
L.
Aravind,2,3
Nick V.
Grishin,1,4 and
Eugene V.
Koonin1,5
1 National Center for Biotechnology Information (NCBI),
National Library of Medicine, National Institutes of Health, Bethesda
Maryland 20894 USA; 2 Department of Biology, Texas A&M
University, College Station, Texas 70843 USA
The RecA/Rad51/DCM1 family of ATP-dependent recombinases plays a
crucial role in genetic recombination and double-stranded DNA break
repair in Archaea, Bacteria, and Eukaryota. DnaB is the replication
fork helicase in all Bacteria. We show here that DnaB shares
significant sequence similarity with RecA and Rad51/DMC1 and two other
related families of ATPases, Sms and KaiC. The conserved region spans
the entire ATP- and DNA-binding domain that consists of about 250 amino
acid residues and includes 7 distinct motifs. Comparison with the
three-dimensional structure of Escherichia coli RecA and phage
T7 DnaB (gp4) reveals that the area of sequence conservation includes
the central parallel  -sheet and most of the connecting helices and
loops as well as a smaller domain that consists of a amino-terminal
helix and a carboxy-terminal -meander. Additionally, we show that
animals, plants, and the malarial Plasmodium but not
Saccharomyces cerevisiae encode a previously undetected DnaB
homolog that might function in the mitochondria. The DnaB homolog from
Arabidopsis also contains a DnaG-primase domain and the DnaB
homolog from the nematode seems to contain an inactivated version of
the primase. This domain organization is reminiscent of bacteriophage
primases-helicases and suggests that DnaB might have been horizontally
introduced into the nuclear eukaryotic genome via a phage vector. We
hypothesize that DnaB originated from a duplication of a RecA-like
ancestor after the divergence of the bacteria from Archaea and
eukaryotes, which indicates that the replication fork helicases in
Bacteria and Archaea/Eukaryota have evolved independently.
3
Present address: National Center for Biotechnology
Information, National Library of Medicine, National Institutes of
Health, Bethesda, Maryland 20894 USA.
4
Present address: Department of Biochemistry,
University of Texas Southwestern Medical Center, Dallas, Texas 75235 USA.
5
Corresponding author.
10:5-16 ©2000 by Cold Spring Harbor Laboratory Press ISSN 1088-9051/00 $5.00
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