PDBsum entry 3c6h

Viral protein

PDB id: 3c6h

Contents

Protein chains

182 a.a.

Metals

_MG ×2

Waters ×96

References listed in PDB file

Key reference

Title

The structure of the phage t4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.

Authors

S.Sun, K.Kondabagil, B.Draper, T.I.Alam, V.D.Bowman, Z.Zhang, S.Hegde, A.Fokine, M.G.Rossmann, V.B.Rao.

Ref.

Cell, 2008, 135, 1251-1262. [DOI no: 10.1016/j.cell.2008.11.015]

PubMed id

19109896

Abstract

Viral genomes are packaged into "procapsids" by powerful molecular motors. We report the crystal structure of the DNA packaging motor protein, gene product 17 (gp17), in bacteriophage T4. The structure consists of an N-terminal ATPase domain, which provides energy for compacting DNA, and a C-terminal nuclease domain, which terminates packaging. We show that another function of the C-terminal domain is to translocate the genome into the procapsid. The two domains are in close contact in the crystal structure, representing a "tensed state." A cryo-electron microscopy reconstruction of the T4 procapsid complexed with gp17 shows that the packaging motor is a pentamer and that the domains within each monomer are spatially separated, representing a "relaxed state." These structures suggest a mechanism, supported by mutational and other data, in which electrostatic forces drive the DNA packaging by alternating between tensed and relaxed states. Similar mechanisms may occur in other molecular motors.

Figure 1.
Figure 1. The Bacteriophage T4 DNA Packaging Machine
(A) The T4 procapsid during DNA packaging.
(B) The packaging motor consists of the dodecameric portal protein gp20 and the large terminase gp17. The gp17 molecule has an N-terminal domain (gp17 N), which hydrolyzes ATP, and a C-terminal domain (gp17 C), which has nuclease activity and a DNA translocation function.
(C) A stereo ribbon diagram of the RB49 gp17 C-terminal domain crystal structure with α helices colored in cyan, β sheets silver, and loops brown. The termini are labeled as N and C, and selected amino acids are numbered. A flexible loop L2, shown as a dotted line, was not seen in the electron density. A magnesium ion was detected in the electron density and is shown as a purple sphere. Conserved acidic residues are shown in ball-and-stick form.
(D) A stereo ribbon diagram of the T4 gp17 crystal structure with α helices colored green in the N-terminal subdomain I, yellow in the N-terminal subdomain II, and cyan in the C-terminal domain. The β sheets are colored silver, and loops are dark yellow. Selected amino acids are numbered. Catalytic residues in the ATPase and nuclease active centers are shown in ball-and-stick form, and a bound phosphate ion is shown as cyan and red spheres.
The ribbon diagrams were generated with the Chimera program (Pettersen et al., 2004).

Figure 2.
Figure 2. Interactions among the Motor Components during DNA Translocation
In all three panels, gp17 N-terminal subdomain I (N-sub I) is colored green, subdomain II (N-sub II) yellow, and C-terminal domain cyan. (A) was generated with the Chimera program, and (B) and (C) were generated with the CCP4mg program (Potterton et al., 2004).
(A) A model of B-form polyA-polyT DNA molecule is shown bound to the T4 gp17 in the packaging mode. Potential interactions between the gp17 molecule and the DNA are shown as dotted lines in the zoomed view.
(B) Open book view of the gp17 N- and C-terminal domain interactions showing charge complementarity. Positively charged, negatively charged, and hydrophobic surfaces in the contact areas are colored blue, red, and white, respectively. Charged residues in the contact areas are labeled. Contact areas are defined by atoms less than 4.5 Å apart between the N- and C-terminal domains.
(C) Stereo diagram of residues in the N- and C-terminal domains contact areas. Oxygen and nitrogen atoms are colored red and blue, respectively.

The above figures are reprinted by permission from Cell Press: Cell (2008, 135, 1251-1262) copyright 2008.