Link to this post | posted 11 Apr, 2019 03:33

GregFrederick@letu.edu

We are finishing annotations of seven P1 subcluster phages this semester. Yes. You read correctly. It's one of those years… We have identified the typical Terminase small subunit in P1s (gp1) and the typical P1 Terminase large subunit (gp2). In finishing gene analysis, we also found a third gene (gp68 in Phalm, Kilkor and Meggido) that hits various 'Terminase large subunit' proteins multiple times, three with a P value of >90%. The HHPred report is here: https://toolkit.tuebingen.mpg.de/#/jobs/Phalm68 1 5OE8_B Large subunit terminase; large terminase, VIRAL PROTEIN; 2.2A {Deep-sea thermophilic phage D6E} 91.72 2.5 7.7 78 430 2 PF04466.13 ; Terminase_3 ; Phage terminase large subunit 90.65 4 6.9 78 202 3 4ZNK_A Phage terminase large subunit; DNA Translocation, VIRAL PROTEIN; HET: SO4; 1.931A {Thermus phage P7426} 90.53 3.9 7.1 77 274 QUESTIONS: I cannot see why a phage might have more than one Terminase large subunit gene. But it looks very real based on HHPred analysis. Can/should we call the function as such? Is there some other explanation? Is there a reason why a phage might benefit from carrying an alternative Terminase presumably with an alternative endonuclease function? To call function or not to call? That is the question. Edited 11 Apr, 2019 03:35

Link to this post | posted 11 Apr, 2019 17:52
debbie	Greg, Without looking, could your terminase,large subunits be hitting different parts of terminase? so you have a modular configuration of as in Auxillium gp2 and gp3, with one gene matching ATPase domain and the other matching a nuclease domain? debbie

Link to this post | posted 11 Apr, 2019 18:16

GregFrederick@letu.edu

I believe gp2 has both ATPase and endonuclease functions. I am running to a full afternoon of classes. So I will have to check after. The top three hits for gp68 (that in question) range in 18-28% coverage. So they may be hitting domains within these other distally related terminase proteins (and not ours)? Those hits are here to make it easier for you to take a look. Thanks. 1. https://www.rcsb.org/structure/5OE8 2. http://pfam.xfam.org/family/PF04466.13#tabview=tab0 3. https://www.rcsb.org/structure/4ZNK The actual HHPred report is here: https://toolkit.tuebingen.mpg.de/#/jobs/Phalm68 Thanks again. Greg

Link to this post | posted 11 Apr, 2019 18:43
debbie	Greg, Again I haven't looked, a 28% hit to terminase could be a DNA binding domain, an ATPase domain, or a nuclease domain hit. This may not even be related to a terminase. Let me know if you really need me to look.

Link to this post | posted 12 Apr, 2019 00:04

GregFrederick@letu.edu

Thanks Debbie, I don't think you need to investigate further. It seems we had a student-faculty communication breakdown. They originally reported an HHPred report with a 94% coverage. Their calculations were based on 94% of the Phalm gp68 protein aligning with the HHPred target hit. My calculations (above) were the % coverage by the Phalm gp68 protein of the HHPred hit. The Phalm gp68 only covers 18-28% of the hits above. After we discussed, I realized that even though we have a P value of 90-92 in each case, the gp68 protein is only 84aa in length. It is not large enough to be a "terminase large subunit" protein. It probably does hit one domain. But,from the HHPred results, it is not obvious which domain that it might be. We'll try to dig a little deeper. Thanks.

Link to this post | posted 12 Apr, 2019 00:31

GregFrederick@letu.edu

All the hits ID'd as "Teriminase Large Subunit" are in the N-terminus of the proteins. After reading this: Structure of the large terminase from a hyperthermophilic virus reveals a unique mechanism for oligomerization and ATP hydrolysis. Xu, R.G., Jenkins, H.T., Antson, A.A., Greive, S.J. (2017) Nucleic Acids Res. 45: 13029-13042 PubMed: 29069443 Search on PubMed DOI: 10.1093/nar/gkx947 Primary Citation of Related Structures: 5OEE, 5OEB, 5OEA, 5OE9 PubMed Abstract: The crystal structure of the large terminase from the Geobacillus stearothermophilus bacteriophage D6E shows a unique relative orientation of the N-terminal adenosine triphosphatase (ATPase) and C-terminal nuclease domains. This monomeric 'initiation' state with the two domains 'locked' together is stabilized via a conserved C-terminal arm, which may interact with the portal protein during motor assembly, as predicted for several bacteriophages. . . . . It seems we are hitting the "ATP Binding Cassette" region. Some of the lower level HHPred hits indicate weak hits to ABCs or ATPases in other proteins. Edited 12 Apr, 2019 00:34