The C-terminal domain of the bacteriophage T4 terminase docks on the prohead portal clip region during DNA packaging

Dixit, Aparna Banerjee; Ray, Krishanu; Thomas, Julie A.; Black, Lindsay W.

doi:10.1016/j.virol.2013.07.011

Cited by 27 publications

(40 citation statements)

References 47 publications

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“…However, this fitting positions the ATPase domain ring distal to the capsid, whereas the nuclease domains interact with portal (Fig. S4E), an interaction that has been observed recently (10). Thus, our revised TerL ring model is a different arrangement than that previously proposed.…”

Section: Resultsmentioning

confidence: 64%

“…Although many ATPase rings are asymmetrical during function (12, 37), we assume fivefold symmetry for simplicity. Regardless, most ringed ATPase structures were first modeled as symmetrical assemblies (32,38), and these models were refined later to show asymmetry during function (9,10,12,37). After docking of the ATPase ring, we used the full-length crystal structure of T4-TerL (8) to orient a homology model of the P74-26 nuclease domain, which results in minimal steric clashes between the two domains.…”

Section: Resultsmentioning

confidence: 99%

“…Cryoelectron microscopy (cryo-EM) studies indicate that a pentamer of TerL subunits attaches to the capsid by binding to a dodecameric assembly called portal (8). However, there are conflicting reports as to the orientation of TerL relative to portal during packaging (8)(9)(10).…”

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confidence: 99%

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Structure and mechanism of the ATPase that powers viral genome packaging

Hilbert

Hayes

Stone

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

171

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Many viruses package their genomes into procapsids using an ATPase machine that is among the most powerful known biological motors. However, how this motor couples ATP hydrolysis to DNA translocation is still unknown. Here, we introduce a model system with unique properties for studying motor structure and mechanism. We describe crystal structures of the packaging motor ATPase domain that exhibit nucleotide-dependent conformational changes involving a large rotation of an entire subdomain. We also identify the arginine finger residue that catalyzes ATP hydrolysis in a neighboring motor subunit, illustrating that previous models for motor structure need revision. Our findings allow us to derive a structural model for the motor ring, which we validate using small-angle X-ray scattering and comparisons with previously published data. We illustrate the model's predictive power by identifying the motor's DNA-binding and assembly motifs. Finally, we integrate our results to propose a mechanistic model for DNA translocation by this molecular machine.ouble-stranded DNA (dsDNA) viruses ranging from bacteriophages to the human pathogens of the herpesvirus family form infectious virions by packaging their genomes into preformed procapsids using a powerful ATPase machine (1). The viral genome packaging motor is a multicomponent molecular machine that must complete several tasks in sequential order, the foremost of which is the ATP-dependent pumping of viral DNA into the procapsid (Fig. 1A). Because the DNA progresses from a flexible state to a semicrystalline state as it fills the capsid interior, the motor pumps against a tremendous force. The pressures inside the filled capsid are estimated to reach 60-70 atm (2, 3), equivalent to 10-fold higher than a bottle of champagne. Thus, the viral packaging motor represents one of the most powerful biological motors known (2, 4).The central component of the packaging motor is the ATPase subunit, which drives DNA translocation. The ATPase subunit is a member of the additional strand, conserved glutamate (ASCE) superfamily of ATPases (5). In herpesviruses, as well as many bacteriophages, this ATPase is from a specific clade of the ASCE family called the terminase family (1, 6). In viruses that use a terminase-type motor for genome packaging, the motor consists of several proteins that assemble into homomeric rings (7) (Fig. 1A). The large terminase (TerL) protein harbors the motor's two enzymatic activities (7): the ATPase activity that pumps DNA into the capsid and an endonuclease domain that cleaves packaged DNA from the remaining concatemeric DNA when the capsid is full. Cryoelectron microscopy (cryo-EM) studies indicate that a pentamer of TerL subunits attaches to the capsid by binding to a dodecameric assembly called portal (8). However, there are conflicting reports as to the orientation of TerL relative to portal during packaging (8-10).A structural model for the bacteriophage T4 TerL ring has been previously proposed (8) with these salient features: (i) the nuclease domains...

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Section: Resultsmentioning

confidence: 64%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Structure and mechanism of the ATPase that powers viral genome packaging

Hilbert

Hayes

Stone

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

171

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“…The portal’s grip is then released while the motor’s grip is retained, resulting in relaxation of the DNA back to the B form and entry of ~2 bp into the capsid. A number of observations on the T4 motor are consistent with this model (83, 98, 99). For instance, intercalating compounds tightly bound to DNA are expelled during DNA translocation, which might be due to DNA crunching.…”

Section: Dna Translocationmentioning

confidence: 54%

“…These studies are consistent with the presence of a portal-binding site in the central region of gp17. On the other hand, fluorescence resonance energy transfer studies suggested that a fluorescent probe attached to the C terminus of gp17 is closer in distance to the N terminus of the portal than is another fluorescent probe attached to the N terminus of gp17, which led to the prediction of an opposite orientation (83). In phage SPP1, the C-terminal domain but not the N-terminal domain of TerL (gp2) bound to the prohead portal (38).…”

Section: Dna Translocationmentioning

confidence: 99%

Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses

2015

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Translocation of viral double-stranded DNA (dsDNA) into the icosahedral prohead shell is catalyzed by TerL, a motor protein that has ATPase, endonuclease, and translocase activities. TerL, following endonucleolytic cleavage of immature viral DNA concatemer recognized by TerS, assembles into a pentameric ring motor on the prohead’s portal vertex and uses ATP hydrolysis energy for DNA translocation. TerL’s N-terminal ATPase is connected by a hinge to the C-terminal endonuclease. Inchworm models propose that modest domain motions accompanying ATP hydrolysis are amplified, through changes in electrostatic interactions, into larger movements of the C-terminal domain bound to DNA. In phage φ29, four of the five TerL subunits sequentially hydrolyze ATP, each powering translocation of 2.5 bp. After one viral genome is encapsidated, the internal pressure signals termination of packaging and ejection of the motor. Current focus is on the structures of packaging complexes and the dynamics of TerL during DNA packaging, endonuclease regulation, and motor mechanics.

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Human herpesvirus portal proteins: Structure, function, and antiviral prospects

Kornfeind

Visalli

2018

Reviews in Medical Virology

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Herpesviruses (Herpesvirales) and tailed bacteriophages (Caudovirales) package their dsDNA genomes through an evolutionarily conserved mechanism. Much is known about the biochemistry and structural biology of phage portal proteins and the DNA encapsidation (viral genome cleavage and packaging) process. Although not at the same level of detail, studies on HSV-1, CMV, VZV, and HHV-8 have revealed important information on the function and structure of herpesvirus portal proteins. During dsDNA phage and herpesviral genome replication, concatamers of viral dsDNA are cleaved into single length units by a virus-encoded terminase and packaged into preformed procapsids through a channel located at a single capsid vertex (portal). Oligomeric portals are formed by the interaction of identical portal protein monomers. Comparing portal protein primary aa sequences between phage and herpesviruses reveals little to no sequence similarity. In contrast, the secondary and tertiary structures of known portals are remarkable. In all cases, function is highly conserved in that portals are essential for DNA packaging and also play a role in releasing viral genomic DNA during infection. Preclinical studies have described small molecules that target the HSV-1 and VZV portals and prevent viral replication by inhibiting encapsidation. This review summarizes what is known concerning the structure and function of herpesvirus portal proteins primarily based on their conserved bacteriophage counterparts and the potential to develop novel portal-specific DNA encapsidation inhibitors.

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The C-terminal domain of the bacteriophage T4 terminase docks on the prohead portal clip region during DNA packaging

Cited by 27 publications

References 47 publications

Structure and mechanism of the ATPase that powers viral genome packaging

Structure and mechanism of the ATPase that powers viral genome packaging

Mechanisms of DNA Packaging by Large Double-Stranded DNA Viruses

Human herpesvirus portal proteins: Structure, function, and antiviral prospects

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