DNA Polymerase II

A search for other DNA polymerases led to the discovery of E. coli DNA polymerase II and DNA polymerase III in the early 1970s. DNA polymerase II... 

Polymerization subunit only DNA polymerase II shares several subunits with DNA polymerase III, including the (3, y, 8, 8, x, and ip subunits (see Table 25-2),... 

Fig. 26-4A) synthesized DNA normally. This finding stimulated an intensive search for new polymerases. Two were found DNA polymerases II (gene pol B)264 and III. Both are present in amounts less than 25% of that of DNA polymerase I.265 266 Both have properties similar to those of polymerase I, but there are important differences. By now DNA polymerases have been isolated from many organisms, many genes have been cloned and many sequences, both of bacterial and eukaryotic polymerases are known. Comparisons of both sequences and three-dimensional structures,266a/b a few of which are shown in Fig. 27-12, suggest that the polymerases belong to at least six families (Table 27-1). These include the RNA-dependent DNA polymerases known as reverse transcriptases as well as some RNA polymerases.267 2681... 

Exonuclease activities, proofreading, and editing. DNA polymerase I not only catalyzes the growth of DNA chains at the 3 end of a primer strand but also, at about a 10-fold slower rate, the hydrolytic removal of nucleotides from the 3 end (31- 5 exonuclease activity). The same enzyme also catalyzes hydrolytic removal of nucleotides from the 5 end of DNA chains. This latter 5 - 3 exonuclease activity, the DNA polymerase activity, and the 3 -5 exonuclease activity all arise from separate active sites in the protein. DNA polymerases II and III do not catalyze... 

Gillin, F. D., and Nossal, N. G. (1976). Control of mutation frequency by bacteriophage T4 DNA polymerase II. Accuracy of nucleotide selection by the L88 mutator, CB120 antimutator, and wild type phage T4 DNA polymerases. J. Biol. Chem. 251, 5225-5232. 

E. coli DNA polymerase I requires all four deoxynucleoside 5 triphosphates (dNTPs) as precursors, Mg2+, a DNA template and a primer with a 3 -OH end. DNA synthesis occurs in a 5 - 3 direction. DNA polymerase I also has a 3 —>5 exonuclease (proof-reading) activity and a 5 —>3 exonuclease activity. E. coli DNA polymerases II and HI lack the 5 —>3 exonuclease activity. 

E. coli also contains two other DNA polymerases, DNA polymerase II and DNA polymerase III. As with DNA polymerase I, these enzymes also catalyze the template-directed synthesis of DNA from deoxynucleotidyl 5 -triphosphates, need a primer with a free 3 -OH group, synthesize DNA in the 5 —>3 direction, and have 3 —>5 exonuclease activity. Neither enzyme has 5 —>3 exonuclease activity. 

DNA polymerase II is a specialized repair enzyme. Like Pol I, a large number of Pol II molecules reside in the cell (about 100). The enzyme is more processive than Pol I. Pol II has the same editing (3 to 5 ) activity as Pol I, but not the 5 to 3 exonuclease activity. 

The enzyme, which uses unwound, single-stranded DNA as a template, is called a DNA polymerase. There are three distinct DNA polymerases in E. coli DNA polymerase I, II, and III. DNA polymerase I is the most abundant, and DNA polymerase III the least abundant. These two enzymes have important roles in the overall process of DNA replication. The role of DNA polymerase II has not yet been clearly established. 

Other DNA polymerases are known. DNA polymerase II and III are produced by the poZB and dnaA genes of E. coti They are similar to DNA polymerase I in most properties. They differ however, in template preferences. While DNA polymerase I acts best to fill in extended single-stranded regions near double-helical regions, DNA polymerases II and III act optimally on double-stranded DNA templates that have short gaps. 

The E. coli translesion polymerases, DNA polymerases II, IV, and V, are under the control of the SOS system. While DNA polymerases II, IV are involved in translesion synthesis of a few selected types of lesions, DNA polymerase V is the... 

In prokaryotes DNA polymerase I has a 5 — 3 DNA polymerase activity as well as a proof reading capacity to chop out nucleotides in either direction through a 5 — 3 and a 3 — 5 direction exonuclease activity DNA polymerases II and III have 5 — 3 ... 

Rangarajan S, Woodgate R, Goodman ME. A phenotype for enigmatic DNA polymerase II a pivotal role for pol II in replication 76. restart in UV-irradiated Escherichia coli. Proc. Natl. Acad. Sci. 

Fuchs RP, Koffel-Schwartz N, Pelet S, Janel-Bintz R, Napolitano R, Becherel OJ, Broschard TH, Burnouf DY, Wagner J. DNA polymerases II and V mediate respectively mutagenic (-2 frameshift) and error-free bypass of a single N-2-acetylaminofluorene adduct. Biochem. Soc. Trans. 2001 29 191-195. 

The two short stretches of amino-acid sequences of the DNA polymerase from P. furiosus which have been published were aligned with eukaryotic DNA polymerases of the B family to claim another eukaryotic feature of archaebacteria [137]. However, Fig. 11 shows that these amino-acid stretches of P. furiosus DNA polymerase and of other archaebacterial DNA polymerases align as well with E. coli DNA polymerase II, a prokaryotic member of the B family [138]. The presence of family B DNA polymerases in the three domains strongly suggests that the divergence between the DNA polymerases of families A, B and C occurred before the divergence between archaebacteria, eubacteria... 

Polymerase I plays an essential role in the replication process in E. coli, but it is not responsible for the overall polymerization of the replicating strands. The enzyme that accomplishes this is a less abundant enzyme, polymerase III (pol III). (A DNA polymerase II has also been isolated from E. coli, but it probably plays no role in DNA synthesis.) Pol III catalyzes the same polymerization reaction as pot I but has certain distinguishing features. It is a very complex enzyme and is associated with eight other proteins to form the pol III holoenzyme. (The term holoenzyme refers to an enzyme that contains several different subunits and retains some activity even when one or more subunits is missing.) Pol III is similar to pol I in that it has a requirement for a template and a primer but its substrate specificity is much more limited. For a template pol III cannot act at a nick nor can it unwind a helix and carry out strand displacement. The latter deficiency means that an auxiliary system is needed to unwind the helix ahead of a replication fork. Pol III, like pol I, possesses a 3 5 exonuclease activity, which performs the major editing function in DNA replication. Polymerase III also has a y exonuclease activity, but this activity does not seem to play a role in replication. 

A recent study showed that Pol IV binds the (1-clamp to help release a stalled Pol III from the same (1-clamp, leaving Pol IV/(l-clamp at the site of the lesion [101], This process is rapid (t < 15 s). Presumably, this mechanism operates for each translesion synthesis DNA polymerase (II, IV and V), all of which have... 

Qiu, A. and Goodman, M.F. (1997) The Escherichia coli polB locus is identical to dinA, the structural gene for DNA polymerase II. Characterization of Pol... 

Crystallization of DNA polymerase II from Escherichia coli. J. Mol. Biol, 238, 120-122. 

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