PDBsum entry: 1dde

Transferase

PDB id: 1dde

Contents

Protein chain

310 a.a. *

Metals

_Y1 ×4

Waters ×290

* Residue conservation analysis

PDB id:

1dde

Name:

Transferase

Title:

Structure of the dnag catalytic core

Structure:

DNA primase. Chain: a. Fragment: 36 kda catalytic core domain. Synonym: dnag. Engineered: yes

Source:

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

Resolution:

1.70Å R-factor: 0.209 R-free: 0.263

Authors:

J.L.Keck,D.D.Roche,A.S.Lynch,J.M.Berger

Key ref:

J.L.Keck et al. (2000). Structure of the RNA polymerase domain of E. coli primase. Science, 287, 2482-2486. PubMed id: 10741967 DOI: 10.1126/science.287.5462.2482

Date:

09-Nov-99 Release date: 07-Apr-00

Protein chain

P0ABS5  (PRIM_ECOLI) -  DNA primase

Seq: 581 a.a.

Struc: 310 a.a.

 Gene Ontology (GO) functional annotation 

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

DOI no: 10.1126/science.287.5462.2482

Science 287:2482-2486 (2000)

PubMed id: 10741967

Structure of the RNA polymerase domain of E. coli primase.

J.L.Keck, D.D.Roche, A.S.Lynch, J.M.Berger.

ABSTRACT

All cellular organisms use specialized RNA polymerases called "primases" to synthesize RNA primers for the initiation of DNA replication. The high-resolution crystal structure of a primase, comprising the catalytic core of the Escherichia coli DnaG protein, was determined. The core structure contains an active-site architecture that is unrelated to other DNA or RNA polymerase palm folds, but is instead related to the "toprim" fold. On the basis of the structure, it is likely that DnaG binds nucleic acid in a groove clustered with invariant residues and that DnaG is positioned within the replisome to accept single-stranded DNA directly from the replicative helicase.

Selected figure(s)

Figure 3.
Fig. 3. Catalytic region of DnaG-RNAP. (A) Proposed active-site and nucleic acid-binding region of DnaG-RNAP stained to demonstrate locations of all invariant (green) and highly conserved (yellow) surface residues. The figure was generated by GRASP (31). (B) Stereo diagram of the putative active site of DnaG-RNAP in the unliganded form (light blue) and Y2+-bound form (dark blue). Three Y2+ ions are shown as yellow spheres, and a Dy3+ ion is shown as a magenta sphere that superposes with the lower Y2+ ion. The position of a Mg2+ ion bound by the active site of topoisomerase VI (22) (green) is overlaid onto DnaG-RNAP by superposition of the homologous toprim domains. One of the Y2+ sites lies only 2.5 Å apart from each of the other sites, implying that the observed Y2+ sites probably represent an average binding of Y2+ ions about the true Mg2+-binding site (or sites) of DnaG. Five invariant-residue side chains are shown: Glu-265, Asp-309 (both Y2+-liganding), Asp-311, Asp-269, and Asp-345. Experimental electron-density maps indicate that these residues are in single rotamer conformations. (C) Topology diagrams of the M. jannaschii topoisomerase VI (T-VI) (22), DnaG-RNAP, and E. coli DNA polymerase I Klenow fragment (Pol I) (32) metal-binding domains. The orders of secondary-structural elements are indicated alphabetically in lowercase ( helices) and uppercase ( strands) letters. NH[2]- and COOH-termini are indicated in italics, and the location of the "fingers" domain in Pol I is indicated as " ". Hatched circles in each diagram indicate invariant metal-liganding residues (Glu-265, Asp-309 in DnaG-RNAP), while triangles indicate the positions of nearby invariant acidic residues (Asp-269, Asp-311, Asp-345). Although the spatial arrangements of metal-binding residues are similar between toprim and palm folds owing to chemical restraints on metal coordination, more detailed comparisons between the active sites await studies of primase-template complexes.

Figure 4.
Fig. 4. Model for primase structure and function within the replisome. (Inset) Organization of the helicase and primase components of the replisome as observed in the bacteriophage T7 primase-helicase polyprotein (24). Primase (purple) directly abuts the helicase (gold). The lagging-strand DNA is thought to be threaded through the central channel (25, 33). (Left and right panels) Models for the orientation of DnaG with respect to DnaB. DNA is shown in blue with synthesized RNA in red. Regions in gray denote the ZBD and DnaB-ID of full-length DnaG whose positions are inferred from the location of the DnaG-RNAP NH[2]- and COOH-termini. (Left) The primase active site faces away from the central hole of the helicase (26). ssDNA extruded from the helicase must loop back to reach the primase active site. The direction by which the RNA:DNA hybrid is translocated and ssDNA is extruded are the same (red and blue arrows, respectively). (Right) The DnaG active site faces toward the interior hole of the helicase. Two DnaB protomers have been cut away to show the central hole, where ssDNA from DnaB is guided directly into the DnaG catalytic center for transcription of RNA. The directions of RNA:DNA hybrid translocation and incoming ssDNA are opposed (arrows). Such a model suggests that primer size preferences observed in vitro (3) and in vivo (7) could arise, in part, from steric effects between the primase, helicase, and newly synthesized primer. The directionality of nucleic acid binding to DnaG is indicated as discussed in the text; although a model where DnaG-RNAP binds primer-template in a different configuration cannot be entirely excluded, existing observations agree with the orientation shown.

The above figures are reprinted by permission from the AAAs: Science (2000, 287, 2482-2486) copyright 2000.

Figures were selected by an automated process.