| 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)
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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 X
encompass two distinct polymerase enzymes that have similar functionality:
vertebrate polymerase beta (yeast pol 4), and terminal deoxynucleotidyl-
transferase (TdT) (EC 2.7.7.31). The former functions in DNA repair, while
the latter terminally adds single nucleotides to polydeoxynucleotide chains.
Both enzymes catalyse addition of nucleotides in a distributive manner,
i.e. they dissociate after the addition of a single nucleotide.
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].
DNAPOLXBETA is a 6-element fingerprint that provides a signature for the
DNA-polymerase X pol beta-like 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 beta-like proteins but distinguish them from the TdT and X
families - motif 1 spans helix 4; motif 2 straddles helix 10 and strand 1;
motif 3, which corresponds to "motif C", spans strands 3 and 4, and helix 12,
and includes two of the active site Asps; motif 4, which corresponds to
"motif A", encodes strand 7, which also contains an active site Asp; motif 5
spans the terminal section of helix 15; and motif 6 encodes helices 17 and
18. Two iterations on OWL30.1 were required to reach convergence, at which
point a true set comprising 7 sequences was identified. Several partial
matches were also found: two of these, G69172 and YA26_SCHPO, are divergent
family members, and the remainder are members of the TdT family.
An update on SPTR37_9f identified a true set of 5 sequences, and 12
partial matches.
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