1BPD

CRYSTAL STRUCTURE OF RAT DNA POLYMERASE BETA: EVIDENCE FOR A COMMON POLYMERASE MECHANISM

Summary for 1BPD

• Entry DOI: 10.2210/pdb1bpd/pdb
• NMR Information: BMRB: 5208,5209
• Descriptor: DNA POLYMERASE BETA, PHOSPHATE ION (2 entities in total)
• Functional Keywords: nucleotidyltransferase
• Biological source: Rattus norvegicus (Norway rat)
• Cellular location: Nucleus: P06766
• Total number of polymer chains: 1
• Total formula weight: 38483.73

Authors

Sawaya, M.R.,Pelletier, H.,Kumar, A.,Wilson, S.H.,Kraut, J. (deposition date: 1994-04-12, release date: 1994-06-22, Last modification date: 2024-02-07)

Primary citation

Sawaya, M.R.,Pelletier, H.,Kumar, A.,Wilson, S.H.,Kraut, J.
Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.
Science, 264:1930-1935, 1994

PubMed Abstract: Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thumb subdomains arranged to form a DNA binding channel reminiscent of the polymerase domains of the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal 8-kilodalton domain is attached to the fingers subdomain by a flexible hinge. The two invariant aspartates found in all polymerase sequences and implicated in catalytic activity have the same geometric arrangement within structurally similar but topologically distinct palms, indicating that the polymerases have maintained, or possibly re-evolved, a common nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding.

PubMed: 7516581

Experimental method

X-RAY DIFFRACTION (3.6 Å)