SEA-PHAGES | Exonuclease domains of DNA polymerase I

Link to this post \| posted 19 May, 2019 12:09
smolloy123	Hi All, I am trying to assign a function to gp52 of NHagos. Nearly every single homologue of this pham has been assigned the function of DNA polymerase I. But gp52 (residues 13-602 out of 602 amino acids total) very precisely aligns only to the 5'-3' exonuclease and the 3'-5' exonuclease domains (residues 4-604 of the DNA polymerase) of DNA polymerase and does not at all align to the polymerase domain. I've attached the HHPRED alignment (in two batches…it was a long one) and a screen shot of the protein feature view of DNA polymerase gene map of E. coli DNA polymerase I. I would not assign a polymerase function to this gene but rather an exonuclease function. Is there a specific exonuclease name I should use for this gene? And if you agree that this is not a polymerase, do we want to change the name of all the homologues? Thanks! Sally 174Kb

Link to this post | posted 19 May, 2019 12:09

Hi All,
I am trying to assign a function to gp52 of NHagos. Nearly every single homologue of this pham has been assigned the function of DNA polymerase I. But gp52 (residues 13-602 out of 602 amino acids total) very precisely aligns only to the 5'-3' exonuclease and the 3'-5' exonuclease domains (residues 4-604 of the DNA polymerase) of DNA polymerase and does not at all align to the polymerase domain. I've attached the HHPRED alignment (in two batches…it was a long one) and a screen shot of the protein feature view of DNA polymerase gene map of E. coli DNA polymerase I.

I would not assign a polymerase function to this gene but rather an exonuclease function. Is there a specific exonuclease name I should use for this gene? And if you agree that this is not a polymerase, do we want to change the name of all the homologues?

Thanks!
Sally

Link to this post \| posted 19 May, 2019 12:10
smolloy123	Actually there is only the protein map as I could only attach one thing. Attached is the beginning of the HHPRED alignment of gp52 to DNA pol I from E. coli 376Kb

Link to this post \| posted 23 May, 2019 17:54
welkin	Hi Sally– In the second picture you show, the protein is aligning to the crystal structure of the Klenow fragament; which according to the first picture you show, includes the polymerase and the 3'-5' exo domains, but not the 5'-3' exo domain. Correct?

Link to this post \| posted 23 May, 2019 19:25
smolloy123	Hi Welkin, It actually does include a both exonuclease domains and just a smidge of the polymerase domain. I think I need to go the paper for this one. It aligns to residue 604 of the polymerase. Cheers Sally

Link to this post \| posted 23 May, 2019 20:47
welkin	But the back end of Pol I is where the polymerase part is. right? So I see a pretty good full length alignment ( I reran to see all the matches) starting part of the way through Pol I and running through to the end. IF you look farther down the HHPred matches the first domain of the phage protein aligns to solo 3'-5' exos, which is the middle of Pol I. and the back half of ours is a polymerase domain. So the missing bit in the phage gene is the 5'-3'exo, that is at the beginning of E coli pol I.

Link to this post | posted 23 May, 2019 20:47

welkin

But the back end of Pol I is where the polymerase part is. right? So I see a pretty good full length alignment ( I reran to see all the matches) starting part of the way through Pol I and running through to the end.
IF you look farther down the HHPred matches the first domain of the phage protein aligns to solo 3'-5' exos, which is the middle of Pol I. and the back half of ours is a polymerase domain. So the missing bit in the phage gene is the 5'-3'exo, that is at the beginning of E coli pol I.

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Exonuclease domains of DNA polymerase I