1.W.2. The Phage Portal Protein 2 (PPP2) Family
The 90-nm-diameter capsid of coliphage T5 is organized with T=13 icosahedral geometry and encloses a double-stranded DNA genome that measures 121kbp. Its assembly follows a path similar to that of phage HK97 but yielding a larger structure that includes 775 subunits of the major head protein, 12 subunits of the portal protein and 120 subunits of the decoration protein. As for phage HK97, T5 encodes the scaffold function as an N-terminal extension (∆-domain) to the major head protein that is cleaved by the maturation protease after assembly of the initial prohead I form and prior to DNA packaging and capsid expansion. Although the major head protein alone is sufficient to assemble capsid-like particles, the yield is poor and includes many deformed structures. Huet et al. 2016 explored the role of both the portal and the protease in capsid assembly by generating constructs that include the major head protein and a combination of protease (wild type or an inactive mutant) and portal proteins and overexpressing them in E. coli. The results showed that the inactive protease mutant acts to trigger assembly of the major head protein, probably through binding to the ∆-domain, while the portal protein regulates assembly into the correct T=13 geometry. A cryo-electron microscopy reconstruction of prohead I including inactivated protease reveals density projecting from the prohead interior surface toward its center that is compatible with the ∆-domain, as well as additional internal density that has been assigned as the inactivated protease. These results reveal complexity in T5 beyond that of the HK97 system (Huet et al. 2016).
Phage T5 portal protein of 403 aas (Huet et al. 2016). It forms the portal vertex of the capsid and plays a role in governing correct capsid geometry. This portal plays critical roles in capsid assembly, genome packaging, head completion protein attachment, and genome ejection. The portal protein multimerizes as a single ring-shaped homododecamer arranged around a central channel (By similarity). It binds to the terminase subunits to form the packaging machine (Huet et al. 2016).
Portal protein of E. coli bacteriophage T5
Phage portal protein of 426 aas. The third gene upstream from the protease gene encodes the portal protein for phage HK97. The presence of the portal protein is not required for assembly of the capsid protein in this system (Duda et al. 1995).
PPP of Vibrio parahaemolyticus phage HK97
Phage portal protein of 416 aa
PPP of Clostridium botulinum
Uncharacterized protein of 414 aas
UP of Armatimonadetes bacterium CP1_7O (hot springs metagenome)
Phage portal protein of 469 aa
PPP of Bifidobacterium longum
HK97 family phage portal protein of 418 aa
PPP of Fusobacterium nucleatum
Phage portal protein of 433 aa
PPP of Chlorobi bacterium OLB5
Uncharacterized protein of 455 aas
UP of Sulfuricurvum sp. MLSB (wastewater metagenome)
Uncharacterized protein sk1p04 of 378 aas
UP of Lactococcus virus sk1