1.W.10.  The (Enterobacterial Phage T7) Portal Protein 10 (PPP10) Family

The phage T7 portal protein has been structurually ellucidated at 8 Å resolution by cryo EM (Protein Databank acc # 6QWP_A; Agirrezabala et al. 2005).  This protein forms the portal vertex of the capsid which plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection into the host bacterium. The portal protein multimerizes as a single ring-shaped homododecamer arranged around a central channel. The T7 connector is that of a 12-folded toroidal homopolymer with a channel that runs along the longitudinal axis of the particle. The structure of the T7 connector reveals many structural similarities with the connectors from other bacteriophages. Docking of the atomic structure of the varphi29 connector into the three-dimensional reconstruction of T7 connector reveals that the narrow, distal region of the two oligomers are almost identical. This region of the varphi29 connector is involved in DNA translocation, and is composed of an alpha-beta-alpha-beta-beta-alpha motif. A search for alpha-helices in the same region of the T7 three-dimensional map located three alpha-helices in approximately the same position as those of the varphi29 connector. A comparison of the predicted secondary structure of several bacteriophage connectors, including among others T7, varphi29, P22 and SPP1, reveals that, despite the lack of sequence homology, they seem to contain the same alpha-beta-alpha-beta-beta-alpha motif as that present in the varphi29 connector. These results suggest a common architecture related to a basic component of the DNA translocating machinery for several viruses (Agirrezabala et al. 2005).



This family belongs to the Phage Portal Protein (PPP) Superfamily.

 

References:

Agirrezabala, X., J. Martín-Benito, M. Valle, J.M. González, A. Valencia, J.M. Valpuesta, and J.L. Carrascosa. (2005). Structure of the connector of bacteriophage T7 at 8A resolution: structural homologies of a basic component of a DNA translocating machinery. J. Mol. Biol. 347: 895-902.

Liu, X., S. Kong, M. Shi, L. Fu, Y. Gao, and C. An. (2008). Genomic analysis of freshwater cyanophage Pf-WMP3 Infecting cyanobacterium Phormidium foveolarum: the conserved elements for a phage. Microb Ecol 56: 671-680.

Examples:

TC#NameOrganismal TypeExample
1.W.10.1.1

Head-tail connector (Escherichia phage T7 gene product 8) portal protein of 536 aa

PPP of Escherichia phage T7

 
1.W.10.1.2

Bacteriophage head to tail connecting portal protein

PPP of Roseomonas stagni

 
1.W.10.1.3

Phage head-tail adapter portal protein of 553 aas

PPP of Oxalobacteraceae bacterium

 
1.W.10.1.5

Uncharacterized protein of 560 aas

UP of Treponema denticola

 
1.W.10.1.6

Uncharacterized protein of 556 aas

UP of Aminobacter aminovorans

 
Examples:

TC#NameOrganismal TypeExample
1.W.10.2.1

Uncharacterized protein of 517 aa

UP of Fusobacterium varium

 
1.W.10.2.2

Uncharacterized protein of 505 aas

UP of Thermoplasmata archaeon

 
Examples:

TC#NameOrganismal TypeExample
1.W.10.3.1

Phage portal protein of 651 aas from a freshwater cyanophage Pf-WMP3, Infecting the cyanobacterium, Phormidium foveolarum (Liu et al. 2008).

PPP of Phormidium virus WMP3

 
1.W.10.3.2

Head-to-tail joining portal protein of 582 aas

PP of Vibrio phage 1.235.O._10N.261.52.B2

 
1.W.10.3.3

Uncharacterized protein of 688 aas

UP of Acidimicrobiaceae bacterium

 
1.W.10.3.4

Phage portal protein of 702 aas

PPP of Sinorhizobium phage phiM6

 
Examples:

TC#NameOrganismal TypeExample