Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis.
BACKGROUND
In chromosomal DNA replication, DNA primase initiates the synthesis of a dinucleotide on a single-stranded template DNA, and elongates it to form a primer RNA for the replicative DNA polymerase. Although the apo-structure of an archaeal primase has been reported, the mechanism of primer synthesis by the eukaryotic-type primase still remains to be elucidated.


RESULTS
In this study, we present the crystal structure of the eukaryotic-type DNA primase from the hyperthermophilic archaeon (Pyrococcus horikoshii) with the uridine 5'-triphosphate (UTP). In the present primase-UTP complex, the primase binds the triphosphate moiety of the UTP at the active site, which includes Asp95, Asp97, and Asp280, the essential residues for the nucleotidyl transfer reaction.


CONCLUSIONS
The nucleotide binding geometry in this complex explains the previous biochemical analyses of the eukaryotic primase. Based on the complex structure, we constructed a model between the DNA primase and a primer/template DNA for the primer synthesis. This model facilitates the comprehension of the reported features of DNA primase.
Ito
Nobutoshi
N
Cellular Physiology Laboratory, Discovery Research Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
Nureki
Osamu
O
Shirouzu
Mikako
M
Yokoyama
Shigeyuki
S
Hanaoka
Fumio
F
D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004249:DNA Damage; D019915:DNA Primase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D003845:Deoxycytosine Nucleotides / Q000737:chemistry / Q000378:metabolism; D046911:Macromolecular Substances; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D011485:Protein Binding; D043902:Pyrococcus horikoshii / Q000201:enzymology*; D012313:RNA / Q000096:biosynthesis; D016415:Sequence Alignment; D014544:Uridine Triphosphate / Q000737:chemistry* / Q000378:metabolism
D003845:Deoxycytosine Nucleotides; D046911:Macromolecular Substances; C034477:RNA primers; D012313:RNA; D019915:DNA Primase; D014544:Uridine Triphosphate