H
IPR042087

DNA polymerase family B, thumb domain

InterPro entry
Short nameDNA_pol_B_thumb
Overlapping entries
 

Description

DNA is 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 life cycle of a cell. This function is performed by DNA- directed DNA-polymerases
2.7.7.7
) by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA, using a complementary DNA chain as a template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used for the de novo synthesis of a DNA chain. Even though there are 2 different methods of priming, these are mediated by 2 very similar polymerases classes, A and B, with similar methods of chain elongation. A number of DNA polymerases have been grouped under the designation of DNA polymerase family B. Six regions of similarity (numbered from I to VI) are found in all or a subset of the B family 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 that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongation domain, a 3'-5' exonuclease domain
[1]
, a DNA binding domain, and binding domains for both dNTP's and pyrophosphate
[2]
.

This superfamily represents the thumb domain found at the C-terminal of the DNA polymerase family B proteins.

References

1.Crystal structures of an NH2-terminal fragment of T4 DNA polymerase and its complexes with single-stranded DNA and with divalent metal ions. Wang J, Yu P, Lin TC, Konigsberg WH, Steitz TA. Biochemistry 35, 8110-9, (1996). View articlePMID: 8679562

2.Crystallization and preliminary diffraction analysis of a hyperthermostable DNA polymerase from a Thermococcus archaeon. Zhou M, Mao C, Rodriguez AC, Kiefer JR, Kucera RB, Beese LS. Acta Crystallogr. D Biol. Crystallogr. 54, 994-5, (1998). View articlePMID: 9757117

Further reading

3. Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta. Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal AK. Nat Struct Mol Biol 16, 979-86, (2009). PMID: 19718023

4. Structures of an apo and a binary complex of an evolved archeal B family DNA polymerase capable of synthesising highly cy-dye labelled DNA. Wynne SA, Pinheiro VB, Holliger P, Leslie AG. PLoS One 8, e70892, (2013). PMID: 23940661

5. Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism. Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut J. Science 264, 1930-5, (1994). View articlePMID: 7516581

Cross References

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