| Literature References | 1. JUNG, G., LEAVITT, M.C., HSIEH, J-C. AND ITO, J.
Bacteriophage PRD1 DNA polymerase: Evolution of DNA polymerases.
PROC.NATL.ACAD.SCI.U.S.A. 84 8287-8291 (1987).
2. DELARUE, M., POCH, O., TORDO, N., MORAS, D. AND ARGOS, P.
An attempt to unify the structure of polymerases.
PROTEIN ENG. 3(6) 461-467 (1990).
3. GENGA, A., BIANCHI, L. AND FOURY, F.
The nuclear gene MIP1 is strictly required for mitochondrial DNA
replication and mitochondrial DNA polymerase activity.
J.BIOL.CHEM. 261 9328-9332 (1986).
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| Documentation | DNA carries the biological information that instructs cells how to exist
in an ordered fashion: accurate replication is thus one of the most
important events in the cell life cycle. This function is mediated by
DNA-directed DNA-polymerases, which add nucleotide triphosphate (dNTP)
residues to the 5'-end of the growing DNA chain, using a complementary
DNA as template. Small RNA molecules are generally used as primers for
chain elongation, although terminal proteins may also be used.
DNA-dependent DNA-polymerases have been grouped into families, denoted A, B
and X, on the basis of sequence similarities [1,2]. Members of family A,
which includes bacterial and bacteriophage polymerases, share significant
similarity to E.coli polymerase I; hence family A is also known as the pol I
family. The bacterial polymerases also contain an exonuclease activity,
which is coded for in the N-terminal portion. The yeast gamma polymerases
show some similarity to the prokaryotic nuclear polymerases of family A,
but their function is restricted to mitochondrial DNA replication and
repair [3].
Three motifs, A, B and C, as defined by Delarue et al. [2], are seen to be
conserved across all DNA-polymerases, with motifs A and C also seen in RNA-
polymerases. They are centered on invariant residues, and their structural
significance was implied from the Klenlow (E.coli) structure: motif A
contains a strictly-conserved aspartate at the junction of a beta-strand
and an alpha-helix; motif B contains an alpha-helix with positive charges;
and motif C has a doublet of negative charges, located in a beta-turn-beta
secondary structure [2].
DNAPOLG is a 9-element fingerprint that provides a signature for the DNA-
polymerase gamma family. The fingerprint was derived from an initial
alignment of 7 sequences: the motifs were drawn from conserved sections
spanning the full alignment length, focusing on those regions that
characterise the gamma polymerases but distinguish them from the rest of
the pol I family - motif 5 includes part of the region encoded by PROSITE
pattern DNA_POLYMERASE_A (PS00447), which corresponds to "motif B". Two
iterations on OWL30.1 were required to reach convergence, at which point a
true set comprising 10 sequences was identified. A single partial match was
also found, DPOG_CHICK, a chicken gamma polymerase fragment that matches
motifs 4-9.
An update on SPTR37_9f identified a true set of 7 sequences.
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