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cluster J terminases

| posted 17 Aug, 2017 16:00
So this has me intrigued and I took another look at the cluster J terminases. Phyre2 analysis reveals that Klein11 is a DNA packaging protein similar to T4 gp17 (large terminase)- 100% confidence, coverage 77%; based on crystal structures. Klein 11 is homologous to Baka6 which is has a much longer ORF. The N terminal region of Baka6 (not in Klein11) is a intein endonuclease (pi-scei homing endonuclease with protein splicing activity) and the C terminal domain has hits to the t4 gp17 atpase domain. Klein2 is also modeled with 100% confidence to T4 dna packaging protein gp17. So it appears that Klein2 and 11 (as well as Baka 2 and 5) are both large terminase subunits. it doesn't seem that they are different domains of the terminase large subunit. Just to make things more interesting, it doesn't appear that Squint has a 2nd large terminase subunit but it has the version of the large terminase without the intein (Squint10). Klein5 appears to be the small terminase. There is another paper refering to the coiled coil motif in small terminases by Kondabagil and Rao Journal of Molecular Biology Vol358 issue 1 (2006)
Edited 18 Aug, 2017 00:34
| posted 12 May, 2021 20:30
So… I'm encountering this exact issue with J cluster Beem. I see the homing endonuclease in the C-terminal region of gp11 (terminase, large subunit) and the HHPred hits to large terminase in the N-terminal. I've also got gp1 hitting to large terminase (and T4's gp17, etc.) and gp9 (immediately upstream of gp11) hitting to small terminase.

So. What should I actually call these genes? Here's what I'm thinking:
gp1 = NKF; add to notes that "similarity to T4 GP17, DNA packaging protein"
gp9 = terminase, small subunit
gp11 = terminase, large subunit; add to notes "contains intein"

Thoughts or suggestions?

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