Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage φ29 connector particle 1 1Edited by R. Huber

Guasch, Alı́cia; Pous, Joan; Ibarra, Borja; Gomis‐Rüth, F. Xavier; Valpuesta, José M.; Sousa, Natália Carolina de; Carrascosa, José L.; Coll, Miquel

doi:10.1006/jmbi.2001.5278

Cited by 204 publications

(367 citation statements)

References 56 publications

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“…Taking into account that the passing DNA would slip smoothly through the channel, an extended electropositive surface would not be adequate. This has been seen in a channel crossing the structure of a reovirus, which is traversed by a RNA molecule [148], and for the bacteriophage Φ29 connector particle [149,150]. The side of the TrwB channel facing the inner-membrane has an opening of ∼ 22 Å, compatible with the values of 25-30 Å for RecA-like hexameric helicases, through which ssDNA may pass [151].…”

Section: Working Hypothesis For Conjugative T4cpssupporting

confidence: 55%

Coupling Factors in Macromolecular Type-IV Secretion Machineries

Gomis‐Rüth

Sola

Cruz³

et al. 2004

CPD

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Type IV secretion systems (T4SSs) are bacterial multiprotein organelles specialised in the transfer of (nucleo)protein complexes across cell membranes. They are essential for conjugation, bacterial-induced tumour formation in plant cells, as observed in Agrobacterium, toxin secretion, like in Bordetella and Helicobacter, cell-to-cell translocation of virulence factors, and intracellular activity of mammalian pathogens like Legionella. By enabling conjugative DNA delivery, these systems contribute to the spread of antibiotic resistance genes among bacteria. These translocons are made up by 10-15 proteins that are analogous to Vir proteins of Agrobacterium and traverse both membranes and the periplasmic space in between in Gram-negative bacteria. Their secretion substrates range from single-stranded DNA / protein complexes to multicomponent toxins and they are assisted by integral inner-membrane coupling factors, the multimeric type-IV coupling proteins (T4CPs), to connect the macromolecular complexes to be transferred with the secretory conduit. To do so, these T4CPs may be required to localise close to the secretion machinery within the donor cell. The T4CP structural prototype is the hexameric protein TrwB of Escherichia coli conjugative plasmid R388, closely related to Agrobacterium VirD4 protein. It is responsible for coupling the relaxosome with the DNA transport apparatus during cell mating. T4CP family members are related to SpoIIIE/FtsK proteins, essential for DNA pumping during sporulation and cell division. These features suggest possible mechanisms for conjugal T4CP function: as a simple coupler between two molecular machines, as a rotating device to pump DNA through the type-IV transport pore, or as a DNA injector, whereby its central channel would function as part of the transport pore.

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Section: Working Hypothesis For Conjugative T4cpssupporting

confidence: 55%

Coupling Factors in Macromolecular Type-IV Secretion Machineries

Gomis‐Rüth

Sola

Cruz³

et al. 2004

CPD

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“…Tunnel loops and rings of lysines lining the portal channel are found in gp6-related proteins and in other portal structures, suggesting that they play the same DNA-anchoring role in the central channel ( Fig. S4 B-D) (26)(27)(28)(29)(30). These elements are too far from the central channel in the portal of phage P22 for interaction with DNA ( Fig.…”

Section: Resultsmentioning

confidence: 94%

Structural rearrangements in the phage head-to-tail interface during assembly and infection

Chaban

Lurz

Brasilès

et al. 2015

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

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Many icosahedral viruses use a specialized portal vertex to control genome encapsidation and release from the viral capsid. In tailed bacteriophages, the portal system is connected to a tail structure that provides the pipeline for genome delivery to the host cell. We report the first, to our knowledge, subnanometer structures of the complete portal-phage tail interface that mimic the states before and after DNA release during phage infection. They uncover structural rearrangements associated with intimate protein-DNA interactions. The portal protein gp6 of bacteriophage SPP1 undergoes a concerted reorganization of the structural elements of its central channel during interaction with DNA. A network of protein-protein interactions primes consecutive binding of proteins gp15 and gp16 to extend and close the channel. This critical step that prevents genome leakage from the capsid is achieved by a previously unidentified allosteric mechanism: gp16 binding to two different regions of gp15 drives correct positioning and folding of an inner gp16 loop to interact with equivalent loops of the other gp16 subunits. Together, these loops build a plug that closes the channel. Gp16 then fastens the tail to yield the infectious virion. The gatekeeper system opens for viral genome exit at the beginning of infection but recloses afterward, suggesting a molecular diaphragm-like mechanism to control DNA efflux. The mechanisms described here, controlling the essential steps of phage genome movements during virus assembly and infection, are likely to be conserved among long-tailed phages, the largest group of viruses in the Biosphere.DNA gatekeeper | viral infection | bacteriophage | allosteric mechanism | hybrid methods

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“…Many of these features in DNA-packaging are also shared by adenoviruses (6). The x-ray structures of the catalytic component from bacteriophage T4 and the portals from various phages were previously described (7)(8)(9)(10). However, it is not known how the terminases are assembled and how they interact with the portals and procapsids.…”

mentioning

confidence: 99%

Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine

Zhao

Finch

Sequeira

et al. 2010

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

101

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In herpesviruses and many bacterial viruses, genome-packaging is a precisely mediated process fulfilled by a virally encoded molecular machine called terminase that consists of two protein components: A DNA-recognition component that defines the specificity for packaged DNA, and a catalytic component that provides energy for the packaging reaction by hydrolyzing ATP. The terminase docks onto the portal protein complex embedded in a single vertex of a preformed viral protein shell called procapsid, and pumps the viral DNA into the procapsid through a conduit formed by the portal. Here we report the 1.65 Å resolution structure of the DNA-recognition component gp1 of the Shigella bacteriophage Sf6 genomepackaging machine. The structure reveals a ring-like octamer formed by interweaved protein monomers with a highly extended fold, embracing a tunnel through which DNA may be translocated. The N-terminal DNA-binding domains form the peripheral appendages surrounding the octamer. The central domain contributes to oligomerization through interactions of bundled helices. The C-terminal domain forms a barrel with parallel beta-strands. The structure reveals a common scheme for oligomerization of terminase DNA-recognition components, and provides insights into the role of gp1 in formation of the packaging-competent terminase complex and assembly of the terminase with the portal, in which ring-like protein oligomers stack together to form a continuous channel for viral DNA translocation.terminase | DNA-packaging | oligomer | bacteriophage | protein:DNA interaction I n many tailed double-stranded DNA (dsDNA) bacteriophages and herpesvirus, the newly synthesized viral DNA in the infected host cell is present as a concatemer that is comprised of multiple copies of unit-length genome. The concatemeric DNA is packaged into a preformed capsid precursor termed procapsid through a channel formed by a portal protein complex embedded in a unique vertex of the procapsid (1-5). The DNApackaging process involves a precisely coordinated sequence of molecular events, driven by a molecular machine called terminase consisting of two proteins: A DNA-recognition component and a catalytic component, also known as the "small" and "large" subunit, respectively. The terminase specifically binds to concatemeric viral DNA through the DNA-recognition component and cleaves it using the catalytic component, generating a new terminus for the DNA. This terminus is threaded through the portal protein channel embedded in the procapsid, and the catalytic component pumps the DNA into the procapsid in an ATP-dependent manner. When an appropriate amount of DNA is inserted, the terminase cuts the DNA again, dissociates from the procapsid, and can start the next cycle of DNA-packaging. Many of these features in DNA-packaging are also shared by adenoviruses (6). The x-ray structures of the catalytic component from bacteriophage T4 and the portals from various phages were previously described (7-10). However, it is not known how the terminases are assembled and h...

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Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage φ29 connector particle 1 1Edited by R. Huber

Cited by 204 publications

References 56 publications

Coupling Factors in Macromolecular Type-IV Secretion Machineries

Coupling Factors in Macromolecular Type-IV Secretion Machineries

Structural rearrangements in the phage head-to-tail interface during assembly and infection

Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine

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