Replicative DNA polymerases

Abstract

Replicative DNA polymerases are essential for the replication of the genomes of all living organisms. On the basis of sequence similarities they can be classified into three types. Type A polymerases are homologous to bacterial polymerases I, Type B comprises archaebacterial DNA polymerases and eukaryotic DNA polymerase alpha, and the bacterial polymerase III class make up type C. Structures have been solved for several type A and B polymerases, which share a similar architecture. The structure of type C is not yet known. The catalytic mechanism of all three types involves two metal-ion-binding acidic residues in the active site. Replicative polymerases are constitutively expressed, but their activity is regulated through the cell cycle and in response to different growth conditions.

Figure 1

Logo representation of DNA polymerase domains from representative polymerase sequences. The sequences were extracted from SwissProt links in Prosite [3] to the DNA polymerase type A (PS00447) and DNA polymerase type B (PS00116) families. The families were initially found using 'DNA polymerase' as keyword. Sequence logos show the relative representation of the different amino acids at each sequence position in terms of the size of the appropriate letter in the single-letter amino acid code; the largest letters are the most conserved. They were constructed using the online server WebLogo [17]. Type A DNA polymerases (10 sequences) were from E. coli (polA), Bacillus subtilis, Thermus aquaticus, Aquifex aeolicus, Mycobacterium tuberculosis, phage T3, phage T5, phage T7, mitochondrial Saccharomyces cerevisiae DNA polymerase and mitochondrial Homo sapiens DNA polymerases. Type B DNA polymerases (15 sequences) were from H. sapiens (α and δ), S. cerevisiae (α and δ), Drosophila melanogaster (α), phage T4, phage RB69, Chlorella virus NY-2A, Zea mays plasmid S-1, herpes simplex virus 1, vaccinia virus, African swine fever virus, Archaeoglobus fulgidus, Pyrococcus horikoshii, E. coli (polB).

Figure 2

DNA polymerase protein structures. The figures were generated with the free software Rasmol (RasWin Molecular Graphics, Windows Version 2.4) and files extracted from the Protein Data Bank (PDB) [18]. (a) Bacteriophage T7 DNA polymerase (type A; PDB code: 1t7p) [9]. Blue, catalytic domain; green, 3'-to-5' exonuclease domain. (b)Thermococcus gorgorianus type B DNA polymerase [11] (PDB code: 1tgo). Blue, catalytic domain; green, 3'-to-5' exonuclease domain; orange, amino-terminal domain; yellow, linker region.