Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.
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.
Sawaya
M R
MR
Department of Chemistry, University of California, San Diego 92093-0317.
Pelletier
H
H
Kumar
A
A
Wilson
S H
SH
Kraut
J
J
D000818:Animals; D001665:Binding Sites; D003001:Cloning, Molecular; D003460:Crystallization; D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism; D004256:DNA Polymerase I / Q000737:chemistry* / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism; D003838:Deoxyadenine Nucleotides / Q000737:chemistry / Q000378:metabolism; D003845:Deoxycytosine Nucleotides / Q000737:chemistry / Q000378:metabolism; D054306:Dideoxynucleotides; D054303:HIV Reverse Transcriptase; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012194:RNA-Directed DNA Polymerase / Q000737:chemistry / Q000378:metabolism; D051381:Rats; D011994:Recombinant Proteins / Q000737:chemistry; D014764:Viral Proteins
D003838:Deoxyadenine Nucleotides; D003845:Deoxycytosine Nucleotides; D054306:Dideoxynucleotides; D011994:Recombinant Proteins; D014764:Viral Proteins; C037406:2',3'-dideoxycytidine 5'-triphosphate; D004247:DNA; C062210:bacteriophage T7 RNA polymerase; D054303:HIV Reverse Transcriptase; D012194:RNA-Directed DNA Polymerase; D012321:DNA-Directed RNA Polymerases; D004256:DNA Polymerase I; C026600:2'-deoxyadenosine triphosphate