PDBsum entry 1q57

Transferase

PDB id: 1q57

Contents

Protein chains

(+ 1 more) 483 a.a. *

* Residue conservation analysis

PDB id:

1q57

Name:

Transferase

Title:

The crystal structure of the bifunctional primase-helicase of bacteriophage t7

Structure:

DNA primase/helicase. Chain: a, b, c, d, e, f, g. Engineered: yes. Mutation: yes

Source:

Enterobacteria phage t7. Organism_taxid: 10760. Gene: 4. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Heptamer (from PQS)

Resolution:

3.45Å R-factor: 0.301 R-free: 0.326

Authors:

E.A.Toth,Y.Li,M.R.Sawaya,Y.Cheng,T.Ellenberger

Key ref:

E.A.Toth et al. (2003). The crystal structure of the bifunctional primase-helicase of bacteriophage T7. Mol Cell, 12, 1113-1123. PubMed id: 14636571 DOI: 10.1016/S1097-2765(03)00442-8

Date:

06-Aug-03 Release date: 25-Nov-03

Protein chains

P03692  (PRIM_BPT7) -  DNA helicase/primase from Escherichia phage T7

Seq: 566 a.a.

Struc: 483 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.- - ?????
• Enzyme class 3: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/S1097-2765(03)00442-8

Mol Cell 12:1113-1123 (2003)

PubMed id: 14636571

The crystal structure of the bifunctional primase-helicase of bacteriophage T7.

E.A.Toth, Y.Li, M.R.Sawaya, Y.Cheng, T.Ellenberger.

ABSTRACT

Within minutes after infecting Escherichia coli, bacteriophage T7 synthesizes many copies of its genomic DNA. The lynchpin of the T7 replication system is a bifunctional primase-helicase that unwinds duplex DNA at the replication fork while initiating the synthesis of Okazaki fragments on the lagging strand. We have determined a 3.45 A crystal structure of the T7 primase-helicase that shows an articulated arrangement of the primase and helicase sites. The crystallized primase-helicase is a heptamer with a crown-like shape, reflecting an intimate packing of helicase domains into a ring that is topped with loosely arrayed primase domains. This heptameric isoform can accommodate double-stranded DNA in its central channel, which nicely explains its recently described DNA remodeling activity. The double-jointed structure of the primase-helicase permits a free range of motion for the primase and helicase domains that suggests how the continuous unwinding of DNA at the replication fork can be periodically coupled to Okazaki fragment synthesis.

Selected figure(s)

Figure 1.
Figure 1. Crystallographic Structure of the T7 Primase-Helicase(A) A ribbon diagram of T7 primase-helicase shows that the helicase domains (red) and associated DNA binding loops (yellow) are arranged in a ring with approximate 7-fold rotational symmetry. This view shows the C-terminal side of the ring.(B) A view of the N-terminal side of the ring shows seven primase domains (blue) are loosely arrayed in different orientations on top of the helicase ring (red). The active sites of the primases (gold balls) roughly face the circumference of the ring and point toward the neighboring subunit. One of the primase domains, designated with an orange ball, tilts toward the center of the ring where its active site is positioned for interaction with DNA passing through the central channel.(C) A schematic diagram, oriented as in (B), shows the relative orientations of the primase domains (blue balls with N-terminal “hats”) and their active sites (light blue dots). The inward facing primase domain has an orange hat. The underlying helicase domains (red) are shown with yellow arrows that point toward the helicase active site. Ribbon diagrams were created with the program RIBBONS (Carson, 1997) and rendered with POV-Ray (Amundsen et al., 2000).

Figure 3.
Figure 3. Crown-Shaped Appearance of the T7 Primase-HelicaseA side view of the surface of the primase-helicase shows that the primase domains (top of figure) are swapped onto neighboring helicase domains (bottom), which pack together in a closed ring. An extended “clasp” between the primase and helicase domains packs against the adjacent subunit and contributes most of the contacts between subunits (cf. Figure 4). The primase domains make few contacts with one another and they are oriented differently in all seven subunits (cf. Figure 1). This loose-packed arrangement would allow a DNA template to bind to the primase active site in the gap between adjacent primase domains. The surface rendering was generated with the program MOLMOL (Koradi et al., 1996) and rendered with POV-Ray (Amundsen et al., 2000).

The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 12, 1113-1123) copyright 2003.

Figures were selected by an automated process.