PDBsum entry: 1eqn

Transferase

PDB id: 1eqn

Contents

Protein chains

315 a.a. *

* Residue conservation analysis

PDB id:

1eqn

Name:

Transferase

Title:

E.Coli primase catalytic core

Structure:

DNA primase. Chain: a, b, c, d, e. Fragment: catalytic core. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.90Å R-factor: 0.220 R-free: 0.276

Authors:

M.Podobnik,P.Mcinerney,M.O'Donnell,J.Kuriyan

Key ref:

M.Podobnik et al. (2000). A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases. J Mol Biol, 300, 353-362. PubMed id: 10873470 DOI: 10.1006/jmbi.2000.3844

Date:

05-Apr-00 Release date: 30-Jun-00

Protein chains

P0ABS5  (PRIM_ECOLI) -  DNA primase

Seq: 581 a.a.

Struc: 315 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: DNA metabolic process (1 term)
• Biochemical function: nucleic acid binding (1 term)

DOI no: 10.1006/jmbi.2000.3844

J Mol Biol 300:353-362 (2000)

PubMed id: 10873470

A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases.

M.Podobnik, P.McInerney, M.O'Donnell, J.Kuriyan.

ABSTRACT

Primases synthesize short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. We present the crystal structure of the catalytic unit of a primase enzyme, that of a approximately 320 residue fragment of Escherichia coli primase, determined at 2.9 A resolution. Central to the catalytic unit is a TOPRIM domain that is strikingly similar in its structure to that of corresponding domains in DNA topoisomerases, but is unrelated to the catalytic centers of other DNA or RNA polymerases. The catalytic domain of primase is crescent-shaped, and the concave face of the crescent is predicted to accommodate about 10 base-pairs of RNA-DNA duplex in a loose interaction, thereby limiting processivity.

Selected figure(s)

Figure 1.
Figure 1. The structure of the E. coli primase catalytic domain. (a) A diagram of the domain organization of full-length primase. The residue numbers corresponding to the domain boundaries in the E. coli protein are indicated. (b) Ribbon representation of the structure of the primase catalytic domain. The orientation shown here is similar to that used in most of the Figures in the paper. The b strands are marked with the red numbers (1-12) and a-helices with black letters (A-N). The circles indicate the boundaries of the TOPRIM sub-domain.

Figure 5.
Figure 5. Potential modes of interaction between the primase and nucleic acids. (a) A speculative model for how a newly synthesized RNA-DNA hybrid might interact with the primase. The molecular surface of the primase catalytic domain is shown, colored according to electrostatic potential as in Figure 4(b). An A-form double helix has been placed so as to locate the end of one strand near the metal-binding site, indicated by the yellow ellipse. The shape of the central groove is such that the double helix can extend only up or down along the surface. The groove narrows towards the top, and so the helix was extended downwards. Note that the phosphate backbone of the template strand (blue) runs close to surface regions with positive electrostatic potential (blue). The single-stranded template is extended upwards (broken line) along a region of positive electrostatic potential, generated by highly conserved residues (see Figure 4(a)). The model shown here is not based on any kind of energetic analysis, but represents instead a simple hypothesis that awaits experimental testing. (b) A potential binding site for nucleotides in the TOPRIM domain. A cross-sectional view of the primase is shown, rotated approximately 90° with respect to the view in (a). A deep pocket, lined by conserved surface residues (see Figure 4(a)) can be seen. This pocket is adjacent to the metal-binding site, which is directly behind it in this view. The pocket is large enough to accommodate a purine base, and an adenine residue is shown here merely to illustrate this fact. If such an interaction were to correspond to an actual binding mode for an adenine nucleotide in the initiation of primer synthesis, it would have to swing out of this pocket in order to base-pair with the complementary base in the template strand.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 300, 353-362) copyright 2000.

Figures were selected by an automated process.