The 1.58 Å resolution structure of the DNA-binding domain of bacteriophage SF6 small terminase provides new hints on DNA binding

Benini, Stefano; Chechik, M.; Lombardia, Miguel Ortiz; Polier, Sigrun; Leech, Andrew; Shevtsov, M.B.; Alonso, Juan C.

doi:10.1107/s1744309113004399

Cited by 6 publications

(6 citation statements)

References 37 publications

(56 reference statements)

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“…The crystal structure of the small terminase DBD, comprising residues 1–68, was determined to 1.4 Å resolution (PDB ID: 4ZC3; Figures 1B , 2 ; Supplementary Table S3). In contrast to previous lower-resolution data ( 14 , 59 ), better-defined electron density was observed for terminal residues 6–9 and 60–62. The structure represents a four-helical bundle where helices α2 and α3 form an HTH motif and α4 connects to the central oligomerization domain, as seen in the lower resolution structure of the full length protein (Figure 1A ; ( 14 )).…”

Section: Resultscontrasting

confidence: 99%

DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif

et al. 2015

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The helix-turn-helix (HTH) motif features frequently in protein DNA-binding assemblies. Viral pac site-targeting small terminase proteins possess an unusual architecture in which the HTH motifs are displayed in a ring, distinct from the classical HTH dimer. Here we investigate how such a circular array of HTH motifs enables specific recognition of the viral genome for initiation of DNA packaging during virus assembly. We found, by surface plasmon resonance and analytical ultracentrifugation, that individual HTH motifs of the Bacillus phage SF6 small terminase bind the packaging regions of SF6 and related SPP1 genome weakly, with little local sequence specificity. Nuclear magnetic resonance chemical shift perturbation studies with an arbitrary single-site substrate suggest that the HTH motif contacts DNA similarly to how certain HTH proteins contact DNA non-specifically. Our observations support a model where specificity is generated through conformational selection of an intrinsically bent DNA segment by a ring of HTHs which bind weakly but cooperatively. Such a system would enable viral gene regulation and control of the viral life cycle, with a minimal genome, conferring a major evolutionary advantage for SPP1-like viruses.

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Section: Resultscontrasting

confidence: 99%

DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif

et al. 2015

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“…This domain was not observed in the crystal structure of 44RR TerS [ 59 ] but can be predicted in the amino acid sequence. In SF6 [ 67 , 74 ] and PaP3 [ 68 ], HTHs are connected to the oligomerization core by flexible, protease-susceptible linkers, whereas TerS from the thermophilic phage P76-26 [ 70 ] has HTHs rigidly held together. Unlike the HTH, the oligomerization core varies for the length of the two α-helices and the presence of an inserted β-hairpin that generates a chapel-like cap structure at one end of the channel [ 63 , 67 ].…”

Section: Diversification Of the Ters Fold And Oligomeric State In Bac...mentioning

confidence: 99%

Viral Small Terminase: A Divergent Structural Framework for a Conserved Biological Function

Lokareddy

Hou

et al. 2022

Viruses

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The genome packaging motor of bacteriophages and herpesviruses is built by two terminase subunits, known as large (TerL) and small (TerS), both essential for viral genome packaging. TerL structure, composition, and assembly to an empty capsid, as well as the mechanisms of ATP-dependent DNA packaging, have been studied in depth, shedding light on the chemo-mechanical coupling between ATP hydrolysis and DNA translocation. Instead, significantly less is known about the small terminase subunit, TerS, which is dispensable or even inhibitory in vitro, but essential in vivo. By taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of phage TerSs, in this review, we take an inventory of known TerSs studied to date. Our analysis suggests that TerS evolved and diversified into a flexible molecular framework that can conserve biological function with minimal sequence and quaternary structure conservation to fit different packaging strategies and environmental conditions.

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“…A structural similarity search was carried out with PDBeFOLD (http://www.ebi.ac.uk/msd-srv/ssm) (Krissinel and Henrick, 2004) with default parameters in search of unexpected structural similarity as in (Benini et al, 2013).…”

Section: Sequence Alignments and Structural Comparisonmentioning

confidence: 99%

The crystal structure of Rv2991 from Mycobacterium tuberculosis: An F420 binding protein with unknown function

Benini

Haouz

Proux

et al. 2019

Journal of Structural Biology

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The 1.58 Å resolution structure of the DNA-binding domain of bacteriophage SF6 small terminase provides new hints on DNA binding

Cited by 6 publications

References 37 publications

DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif

DNA recognition for virus assembly through multiple sequence-independent interactions with a helix-turn-helix motif

Viral Small Terminase: A Divergent Structural Framework for a Conserved Biological Function

The crystal structure of Rv2991 from Mycobacterium tuberculosis: An F420 binding protein with unknown function

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