PROSITE documentation PDOC00452

DNA polymerase family X signature

Description:

DNA polymerases (EC 2.7.7.7) can be classified, on the basis of sequence similarity [1], into at least four different groups: A, B, C and X. DNA polymerases that belong to family X are listed below [2]:

  • Vertebrate polymerase β, involved in DNA repair.
  • Yeast polymerase IV (POL4) [3], an enzyme with similar characteristics to that of the mammalian polymerase β.
  • Terminal deoxynucleotidyltransferase (TdT) (EC 2.7.7.31). TdT catalyzes the elongation of polydeoxynucleotide chains by terminal addition. One of the functions of this enzyme is the addition of nucleotides at the junction of rearranged Ig heavy chain and T cell receptor gene segments during the maturation of B and T cells.
  • African Swine Fever virus protein O174L [4].
  • Fission yeast hypothetical protein SpAC2F7.06c.

These enzymes are small (about 40 Kd) compared with other polymerases and their reaction mechanism operates via a distributive mode, i.e. they dissociate from the template-primer after addition of each nucleotide.

As a signature pattern for this family of DNA polymerases, we selected a highly conserved region that contains a conserved arginine and two conserved aspartic acid residues. The latter together with the arginine have been shown [5] to be involved in primer binding in polymerase β.

Last update:

May 2004 / Text revised.

Technical section:

PROSITE method (with tools and information) covered by this documentation:

DNA_POLYMERASE_X, PS00522DNA polymerase family X signature  (PATTERN)
Consensus pattern: G-[SG]-[LFY]-x-R-[GE]-x(3)-[SGCL]-x-D-[LIVM]-D-[LIVMFY](3)-x(2)-[SAP]
The 2 D's and the R are involved in ssDNA binding
Sequences known to belong to this class detected by the pattern: ALL
Other sequence(s) detected in Swiss-Prot: NONE
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
Retrieve the sequence logo from the alignment
Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS00522
Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS00522
Scan Swiss-Prot/TrEMBL entries against PS00522
view ligand binding statistics
Matching PDB structures: 1BPB 1BPD 1BPE 1BPX ... [ALL]

References:

1 AuthorsIto J., Braithwaite D.K.
TitleCompilation and alignment of DNA polymerase sequences.
SourceNucleic Acids Res. 19:4045-4057(1991).
PubMed ID1870963
2 AuthorsMatsukage A., Nishikawa K., Ooi T., Seto Y., Yamaguchi M.
TitleHomology between mammalian DNA polymerase beta and terminal deoxynucleotidyltransferase.
SourceJ. Biol. Chem. 262:8960-8962(1987).
PubMed ID3597402
3 AuthorsPrasad R., Widen S.G., Singhal R.K., Watkins J., Prakash L., Wilson S.H.
TitleYeast open reading frame YCR14C encodes a DNA beta-polymerase-like enzyme.
SourceNucleic Acids Res. 21:5301-5307(1993).
PubMed ID8265341
4 AuthorsYanez R.J., Rodriguez J.M., Nogal M.L., Yuste L., Enriquez C., Rodriguez J.F., Vinuela E.
TitleAnalysis of the complete nucleotide sequence of African swine fever virus.
SourceVirology 208:249-278(1995).
PubMed ID11831707
5 AuthorsDate T., Yamamoto S., Tanihara K., Nishimoto Y., Matsukage A.
TitleAspartic acid residues at positions 190 and 192 of rat DNA polymerase beta are involved in primer binding.
SourceBiochemistry 30:5286-5292(1991).
PubMed ID2036395

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