{PDOC00107}
{PS00116; DNA_POLYMERASE_B}
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* DNA polymerase family B signature *
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Replicative  DNA polymerases (EC  2.7.7.7) are the key enzymes  catalyzing the
accurate  replication of DNA.   They require either a small RNA molecule or  a
protein as a primer for the de novo synthesis of a DNA chain.  On the basis of
sequence similarity,  a  number  of DNA polymerases have been grouped [1 to 7]
under the designation of DNA polymerase family B. These are:

 - Higher eukaryotes polymerases alpha.
 - Higher eukaryotes polymerases delta.
 - Yeast polymerase  I/alpha (gene POL1),  polymerase II/epsilon  (gene POL2),
   polymerase III/delta (gene POL3) and polymerase REV3.
 - Escherichia coli polymerase II (gene dinA or polB).
 - Archaebacterial polymerases.
 - Polymerases of viruses from the herpesviridae family.
 - Polymerases from Adenoviruses.
 - Polymerases from Baculoviruses.
 - Polymerases from Chlorella viruses.
 - Polymerases from Poxviruses.
 - Bacteriophage T4 polymerase.
 - Podoviridae bacteriophages Phi-29, M2 and PZA polymerase.
 - Tectiviridae bacteriophage PRD1 polymerase.
 - Polymerases encoded  on mitochondrial linear  DNA plasmids in various fungi
   and plants  (Kluyveromyces lactis pGKL1 and pGKL2,  Agaricus bitorquis pEM,
   Ascobolus immersus pAI2,  Claviceps purpurea pCLK1,  Neurospora Kalilo  and
   Maranhar, maize S-1, etc).

Six regions of similarity (numbered from I to VI) are found in all or a subset
of the above polymerases.  The most conserved region  (I) includes a conserved
tetrapeptide with  two  aspartate  residues.  Its  function is not  yet known.
However, it  has  been  suggested  [3]  that  it  may be involved in binding a
magnesium ion.    We  selected  this  conserved region as a signature for this
family of DNA polymerases.

-Consensus pattern: [YA]-[GLIVMSTAC]-D-T-D-[SG]-[LIVMFTC]-{LA}-[LIVMSTAC]
-Sequences known to belong to this class detected by the pattern: ALL,  except
 for yeast  polymerase  II/epsilon,  Agaricus  bitorquis  pEM  and  Sulfolobus
 solfataricus polymerase II.
-Other sequence(s) detected in Swiss-Prot: 9.
-Last update: December 2004 / Pattern and text revised.

[ 1] Jung G.H., Leavitt M.C., Hsieh J.-C., Ito J.
     "Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerases."
     Proc. Natl. Acad. Sci. U.S.A. 84:8287-8291(1987).
     PubMed=3479792
[ 2] Bernad A., Zaballos A., Salas M., Blanco L.
     "Structural and functional relationships between prokaryotic and
     eukaryotic DNA polymerases."
     EMBO J. 6:4219-4225(1987).
     PubMed=3127204
[ 3] Argos P.
     "A sequence motif in many polymerases."
     Nucleic Acids Res. 16:9909-9916(1988).
     PubMed=2461550
[ 4] Wang T.S.-F., Wong S.W., Korn D.
     "Human DNA polymerase alpha: predicted functional domains and
     relationships with viral DNA polymerases."
     FASEB J. 3:14-21(1989).
     PubMed=2642867
[ 5] Delarue M., Poch O., Tordo N., Moras D., Argos P.
     "An attempt to unify the structure of polymerases."
     Protein Eng. 3:461-467(1990).
     PubMed=2196557
[ 6] Ito J., Braithwaite D.K.
     "Compilation and alignment of DNA polymerase sequences."
     Nucleic Acids Res. 19:4045-4057(1991).
     PubMed=1870963
[ 7] Braithwaite D.K., Ito J.
     "Compilation, alignment, and phylogenetic relationships of DNA
     polymerases."
     Nucleic Acids Res. 21:787-802(1993).
     PubMed=8451181

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