SEA-PHAGES | Pham 23485 repA/DNA primase polymerase

Link to this post \| posted 20 Jul, 2017 21:33
dbolliva	I am trying to figure out how to call members of this Pham. There are many different functions that have been ascribed to it. I think this is due to the many conserved domains found in the protein as well as the large size. I am attaching a screen shot of the CDD results from when I BLASTed it on the NCBI website. There is a region towards the N-terminus that has a domain similar to primase/polymerases that are mostly eukaryotic/archeal. There is AAA ATPase domain that is also in a region with similarity to the RepA helicase and this also has similarity to DNA repair enzyme radB and also gamma and Tau subunits of DNA polymerase III. In the HHPRED results attached as a screenshot it is clear that there are two regions with different hits. The N-terminal region shows similarity to the primase/polymerase. The other region has the hits to thelicase/AAA/repair proteins. In the structure of the primase polymerase from the plasmid pRN1 found in an archaebacterium, these activities are dependent on the same amino acid residues, suggesting that both of these activities may use the same active site (EMBO Journal 22:2516-2525, Lipps et al). In the archaebacterial plasmid protein the enzyme was shown to have four activities, ATPase, primase, DNA polymerase, and helicase. In the most recent paper I found about this system (Microbiology Open, 2014,Berkner at al. 3:688-701) the authors suggest that this replication protein recognizes the origin of replication, opens stem loop structures in the origin with the helicase activity and then primes and makes a short DNA strand to create a replication fork that the host polymerase can then recognize and replicate. It is now clear why there is a number of different calls made for members of this Pham. Maybe it would make sense to call this a multifunctinal replication protein? I know we don't like nonspecific names, but the alternative might be DNA polymerase/primase/helicase/ ATPase? Edited 20 Jul, 2017 21:34 164Kb 386Kb

Link to this post | posted 20 Jul, 2017 21:33

I am trying to figure out how to call members of this Pham. There are many different functions that have been ascribed to it. I think this is due to the many conserved domains found in the protein as well as the large size. I am attaching a screen shot of the CDD results from when I BLASTed it on the NCBI website. There is a region towards the N-terminus that has a domain similar to primase/polymerases that are mostly eukaryotic/archeal. There is AAA ATPase domain that is also in a region with similarity to the RepA helicase and this also has similarity to DNA repair enzyme radB and also gamma and Tau subunits of DNA polymerase III. In the HHPRED results attached as a screenshot it is clear that there are two regions with different hits. The N-terminal region shows similarity to the primase/polymerase. The other region has the hits to thelicase/AAA/repair proteins.

In the structure of the primase polymerase from the plasmid pRN1 found in an archaebacterium, these activities are dependent on the same amino acid residues, suggesting that both of these activities may use the same active site (EMBO Journal 22:2516-2525, Lipps et al). In the archaebacterial plasmid protein the enzyme was shown to have four activities, ATPase, primase, DNA polymerase, and helicase. In the most recent paper I found about this system (Microbiology Open, 2014,Berkner at al. 3:688-701) the authors suggest that this replication protein recognizes the origin of replication, opens stem loop structures in the origin with the helicase activity and then primes and makes a short DNA strand to create a replication fork that the host polymerase can then recognize and replicate.

It is now clear why there is a number of different calls made for members of this Pham. Maybe it would make sense to call this a multifunctinal replication protein? I know we don't like nonspecific names, but the alternative might be DNA polymerase/primase/helicase/ ATPase?

Edited 20 Jul, 2017 21:34

Link to this post \| posted 31 Jul, 2017 14:57
welkin	Thanks Dave– this is a really helpful analysis of a tricky protein. It sounds like the phage is using a multifunction replication protein like pRN1. I am going to check in with Graham and get an official answer.

Link to this post \| posted 26 Jan, 2023 21:19
afreise	Hello, I have run into the exact same question for a gene in Usavi_draft_58 (see attached PDF with HHpred and CDD results, good hits to multiple different functions). Was there ever a decision made for this type of gene? The pham has a number of different functions called. 153Kb

Link to this post \| posted 26 Jan, 2023 23:45
debbie	Nope, not yet. all help is welcome! debbie

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Pham 23485 repA/DNA primase polymerase