PDBsum entry 1v34

Transferase

PDB id: 1v34

Contents

Protein chain

346 a.a. *

Ligands

UTP

Metals

_ZN

Waters ×21

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: Crystal structure of the pyrococcus horikoshii DNA primase-Utp complex: implications for the mechanism of primer synthesis.
• Authors: N.Ito, O.Nureki, M.Shirouzu, S.Yokoyama, F.Hanaoka.
• Ref.: Genes Cells, 2003, 8, 913-923.
• PubMed id: 14750947

Abstract

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. CONCLUSION: 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.