One thing that we need to agree on from the outset is the scope of this article (or section of an article). The previous version implied that the beta clamp is found both in prokaryotes and eukaryotes. However the usage of the term "beta clamp" in the scientific literature in usually restricted to prokaryotes (i.e., the beta subunit of the prokaryotic DNA polymerase III) while "DNA clamp" is an umbrella term that encompasses both the dimeric prokaryotic and trimeric eukaryotic protein complexes. I have therefore modified the text in this to restrict the scope of the article the prokaryotic protein complex. Boghog ( talk) 04:11, 14 December 2010 (UTC)
The key phrase in what you wrote above is:
The crystal structure of PCNA closely resembles that of the E. coli beta-subunit: a trimer forms a ring that surrounds the DNA. Although the sequence and subunit organization are different from that of the dimeric beta clamp ...
Hence your source also distinguishes the eukaryotic PCNA sliding clamp (which is a trimer) from the E. coli beta clamp (which is a dimer). You are correct when you say the "DNA Pol delta is synonymous with Dna Pol III". The following table is a summary of the three types of sliding clamps and their associated polymerases:
Kingdom | Sliding clamp protein | Aggregation state | Associated polymerase |
---|---|---|---|
Bacteria | beta subunit of pol III | dimer | DNA polymerase III |
Archaea & Eukaryotes | PCNA | trimer | DNA polymerase delta |
Virus | p45 | timer | viral or host |
The eukaryotic PCNA sliding clamp and bacterial beta clamp have very similar but not identical structures when in their functional aggregated state:
Most of what your wrote concerning the beta clamp concerns the beta subunit of the prokaryotic DNA polymerase III and the associated subunits of the prokaryotic polymerase. Hence it would make sense to restrict the subject of this article to prokaryotic beta clamp. Do you agree? Boghog ( talk) 20:05, 21 December 2010 (UTC)
Hay, how are ya, and thanks for all. Re my promised perusal of Pubmed; well, the phrase "2 subunits of 3 domains {beta} versus 3 subunits of 2 domains {PCNA}" will take some time to settle yet we must trust our Sources. I studied your alterations to both Dna clamp - it seems to need to be a permanent fixture - and Betaclamp-Sandbox; I see it as apparent that you want it maintained, too. I'll be delighted to do the proofreading - Next topic - would appear to be the selection of a replacement [with a more 'fond'] name for PCNA. ~ It is also true that 'Dna Clamp' is more descriptive. ~ Have you seen the 'space-filling-model' pictograph of a clamp encircling Dna? ~ It is where my "in terms of genetic expression, this is where rubber meets the road" comment came from. ~ Betaclamp ( talk) 08:18, 28 December 2010 (UTC)
Hi. Re your PCNA pictograph, it is very nice: prior to viewing it I was aware of A-coils and B- sheets - were you as surprised as I to see -'also loops - in green'? Wow.
A) I sent a msg to Adrian about our activities, wanting him to see them; B) Do you have any tasks for me re: your expectations as to the resolution of this; and C) Once again giving "Betaclamp" the once over it seems, without deletions, to be an Article to me. Many thanks. ~ Betaclamp ( talk) 07:23, 13 January 2011 (UTC)
One thing that we need to agree on from the outset is the scope of this article (or section of an article). The previous version implied that the beta clamp is found both in prokaryotes and eukaryotes. However the usage of the term "beta clamp" in the scientific literature in usually restricted to prokaryotes (i.e., the beta subunit of the prokaryotic DNA polymerase III) while "DNA clamp" is an umbrella term that encompasses both the dimeric prokaryotic and trimeric eukaryotic protein complexes. I have therefore modified the text in this to restrict the scope of the article the prokaryotic protein complex. Boghog ( talk) 04:11, 14 December 2010 (UTC)
The key phrase in what you wrote above is:
The crystal structure of PCNA closely resembles that of the E. coli beta-subunit: a trimer forms a ring that surrounds the DNA. Although the sequence and subunit organization are different from that of the dimeric beta clamp ...
Hence your source also distinguishes the eukaryotic PCNA sliding clamp (which is a trimer) from the E. coli beta clamp (which is a dimer). You are correct when you say the "DNA Pol delta is synonymous with Dna Pol III". The following table is a summary of the three types of sliding clamps and their associated polymerases:
Kingdom | Sliding clamp protein | Aggregation state | Associated polymerase |
---|---|---|---|
Bacteria | beta subunit of pol III | dimer | DNA polymerase III |
Archaea & Eukaryotes | PCNA | trimer | DNA polymerase delta |
Virus | p45 | timer | viral or host |
The eukaryotic PCNA sliding clamp and bacterial beta clamp have very similar but not identical structures when in their functional aggregated state:
Most of what your wrote concerning the beta clamp concerns the beta subunit of the prokaryotic DNA polymerase III and the associated subunits of the prokaryotic polymerase. Hence it would make sense to restrict the subject of this article to prokaryotic beta clamp. Do you agree? Boghog ( talk) 20:05, 21 December 2010 (UTC)
Hay, how are ya, and thanks for all. Re my promised perusal of Pubmed; well, the phrase "2 subunits of 3 domains {beta} versus 3 subunits of 2 domains {PCNA}" will take some time to settle yet we must trust our Sources. I studied your alterations to both Dna clamp - it seems to need to be a permanent fixture - and Betaclamp-Sandbox; I see it as apparent that you want it maintained, too. I'll be delighted to do the proofreading - Next topic - would appear to be the selection of a replacement [with a more 'fond'] name for PCNA. ~ It is also true that 'Dna Clamp' is more descriptive. ~ Have you seen the 'space-filling-model' pictograph of a clamp encircling Dna? ~ It is where my "in terms of genetic expression, this is where rubber meets the road" comment came from. ~ Betaclamp ( talk) 08:18, 28 December 2010 (UTC)
Hi. Re your PCNA pictograph, it is very nice: prior to viewing it I was aware of A-coils and B- sheets - were you as surprised as I to see -'also loops - in green'? Wow.
A) I sent a msg to Adrian about our activities, wanting him to see them; B) Do you have any tasks for me re: your expectations as to the resolution of this; and C) Once again giving "Betaclamp" the once over it seems, without deletions, to be an Article to me. Many thanks. ~ Betaclamp ( talk) 07:23, 13 January 2011 (UTC)