PDBsum entry 1ro0

Replication

PDB id: 1ro0

Contents

Protein chain

210 a.a. *

Metals

_ZN ×2

Waters ×208

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of a bifunctional DNA primase-Polymerase.

Authors

G.Lipps, A.O.Weinzierl, G.Von scheven, C.Buchen, P.Cramer.

Ref.

Nat Struct Mol Biol, 2004, 11, 157-162. [DOI no: 10.1038/nsmb723]

PubMed id

14730355

Abstract

Genome replication generally requires primases, which synthesize an initial oligonucleotide primer, and DNA polymerases, which elongate the primer. Primase and DNA polymerase activities are combined, however, in newly identified replicases from archaeal plasmids, such as pRN1 from Sulfolobus islandicus. Here we present a structure-function analysis of the pRN1 primase-polymerase (prim-pol) domain. The crystal structure shows a central depression lined by conserved residues. Mutations on one side of the depression reduce DNA affinity. On the opposite side of the depression cluster three acidic residues and a histidine, which are required for primase and DNA polymerase activity. One acidic residue binds a manganese ion, suggestive of a metal-dependent catalytic mechanism. The structure does not show any similarity to DNA polymerases, but is distantly related to archaeal and eukaryotic primases, with corresponding active-site residues. We propose that archaeal and eukaryotic primases and the prim-pol domain have a common evolutionary ancestor, a bifunctional replicase for small DNA genomes.

Figure 2.
Figure 2. Surface features. (a) Conservation. The solvent-accessible surface is colored in yellow and orange at locations for invariant and conserved residues, respectively, according to Figure 1a. Residues that are essential for DNA polymerase activity are labeled. The view is as in Figure 1b, left. (b) Charge distribution. The surface is colored from negative (red) to positive charge (blue). Residues involved in DNA binding are labeled. The view on the right is related to that on the left by a 20° rotation about a vertical axis. The dashed circle shows the presumed location of the DNA duplex emanating from the active site toward the reader.

Figure 4.
Figure 4. Comparison of the prim-pol domain with Pfu archaeal primase^3. Catalytic domains are in silver and structurally conserved regions are highlighted in green. Four equivalent residues (three acidic active-site residues and a neighboring histidine) are in orange. The archaeal primase contains an additional species-specific domain (blue).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 157-162) copyright 2004.