PDBsum entry: 1nui

Replication

PDB id: 1nui

Contents

Protein chains

242 a.a. *

Metals

_MG ×4

_ZN ×2

Waters ×14

* Residue conservation analysis

PDB id:

1nui

Name:

Replication

Title:

Crystal structure of the primase fragment of bacteriophage t helicase protein

Structure:

DNA primase/helicase. Chain: a, b. Fragment: residues 1-255. Engineered: yes. Mutation: yes

Source:

Enterobacteria phage t7. Organism_taxid: 10760. Gene: 4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.90Å R-factor: 0.237 R-free: 0.277

Authors:

M.Kato,T.Ito,G.Wagner,C.C.Richardson,T.Ellenberger

Key ref:

M.Kato et al. (2003). Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis. Mol Cell, 11, 1349-1360. PubMed id: 12769857 DOI: 10.1016/S1097-2765(03)00195-3

Date:

31-Jan-03 Release date: 27-May-03

Protein chains

P03692  (PRIM_BPT7) -  DNA primase/helicase

Seq: 566 a.a.

Struc: 242 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H₂O = ADP + phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biochemical function: zinc ion binding (3 terms)

reference

DOI no: 10.1016/S1097-2765(03)00195-3

Mol Cell 11:1349-1360 (2003)

PubMed id: 12769857

Modular architecture of the bacteriophage T7 primase couples RNA primer synthesis to DNA synthesis.

M.Kato, T.Ito, G.Wagner, C.C.Richardson, T.Ellenberger.

ABSTRACT

DNA primases are template-dependent RNA polymerases that synthesize oligoribonucleotide primers that can be extended by DNA polymerase. The bacterial primases consist of zinc binding and RNA polymerase domains that polymerize ribonucleotides at templating sequences of single-stranded DNA. We report a crystal structure of bacteriophage T7 primase that reveals its two domains and the presence of two Mg(2+) ions bound to the active site. NMR and biochemical data show that the two domains remain separated until the primase binds to DNA and nucleotide. The zinc binding domain alone can stimulate primer extension by T7 DNA polymerase. These findings suggest that the zinc binding domain couples primer synthesis with primer utilization by securing the DNA template in the primase active site and then delivering the primed DNA template to DNA polymerase. The modular architecture of the primase and a similar mechanism of priming DNA synthesis are likely to apply broadly to prokaryotic primases.

Selected figure(s)

Figure 2.
Figure 2. Metal Binding in the Active Site of T7 PrimaseA stereo view of the primase active site is shown with the experimentally phased electron density superimposed, contoured at 1 σ. The conserved acidic residues of primase motifs V and VI are labeled and they chelate two Mg^2+ ions (gold spheres). A nearby water molecule (red sphere) is coordinated by one of the Mg^2+ ions.

Figure 3.
Figure 3. Modular Architecture of T7 and DnaG Primases(A) The structure of T7 primase has features resembling the ZBD of Bst primase (Pan and Wigley, 2000) and the RPD from E. coli DnaG (Keck et al. 2000 and Podobnik et al. 2000). The structurally conserved regions are colored as follows: the zinc ribbon motif (red), the N-terminal subdomain of the RPD (yellow), and the C-terminal TOPRIM fold (blue). The bound metal ions in T7 primase are depicted as silver spheres. Bst ZBD has additional α helices (gray) flanking the conserved zinc ribbon motif. A unique subdomain at the C terminus of DnaG (gray) supports its interactions with the DnaB helicase.(B) A topological comparison of the primases. The subdomains are colored as (A), and the secondary structures are depicted as arrows for β strands and cylinders for α helices and 3[10] helices. The broken lines indicate disordered regions of T7 primase. The dotted line between Bst ZBD and the RPD of E. coli DnaG indicates the predicted connection between these domains.

The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 11, 1349-1360) copyright 2003.

Figures were selected by an automated process.