1qqc
From Proteopedia
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CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK
Overview
BACKGROUND: Members of the Pol II family of DNA polymerases are, responsible for chromosomal replication in eukaryotes, and carry out, highly processive DNA replication when attached to ring-shaped, processivity clamps. The sequences of Pol II polymerases are distinct from, those of members of the well-studied Pol I family of DNA polymerases. The, DNA polymerase from the archaebacterium Desulfurococcus strain Tok (D. Tok, Pol) is a member of the Pol II family that retains catalytic activity at, elevated temperatures. RESULTS: The crystal structure of D. Tok Pol has, been determined at 2.4 A resolution. The architecture of this Pol II type, DNA polymerase resembles that of the DNA polymerase from the bacteriophage, RB69, with which it shares less than approximately 20% sequence identity., As in RB69, the central catalytic region of the DNA polymerase is located, within the 'palm' subdomain and is strikingly similar in structure to the, corresponding regions of Pol I type DNA polymerases. The structural, scaffold that surrounds the catalytic core in D. Tok Pol is unrelated in, structure to that of Pol I type polymerases. The 3'-5' proofreading, exonuclease domain of D. Tok Pol resembles the corresponding domains of, RB69 Pol and Pol I type DNA polymerases. The exonuclease domain in D. Tok, Pol is located in the same position relative to the polymerase domain as, seen in RB69, and on the opposite side of the palm subdomain compared to, its location in Pol I type polymerases. The N-terminal domain of D. Tok, Pol has structural similarity to RNA-binding domains. Sequence alignments, suggest that this domain is conserved in the eukaryotic DNA polymerases, delta and epsilon. CONCLUSIONS: The structure of D. Tok Pol confirms that, the modes of binding of the template and extrusion of newly synthesized, duplex DNA are likely to be similar in both Pol II and Pol I type DNA, polymerases. However, the mechanism by which the newly synthesized product, transits in and out of the proofreading exonuclease domain has to be quite, different. The discovery of a domain that seems to be an RNA-binding, module raises the possibility that Pol II family members interact with, RNA.
About this Structure
1QQC is a Single protein structure of sequence from Desulfurococcus sp. tok with SO4 and MG as ligands. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.
Reference
Crystal structure of an archaebacterial DNA polymerase., Zhao Y, Jeruzalmi D, Moarefi I, Leighton L, Lasken R, Kuriyan J, Structure. 1999 Oct 15;7(10):1189-99. PMID:10545321
Page seeded by OCA on Wed Nov 21 00:53:28 2007
