User talk:Betaclamp/Sandbox

Article scope

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 edit to restrict the scope of the article the prokaryotic protein complex. Boghog (talk) 04:11, 14 December 2010 (UTC)[reply]

The tome GENES VI never made such a distinction. Lines 6 & 7 of Betaclamp [sandbox] - Mechanism states " That intermediary is the beta clamp - two parts in prokaryotes, three parts in eukaryotes." and were taken directly from this tome. ~ Betaclamp (talk) 06:20, 18 December 2010 (UTC) P. S. again no mention of a Dna clamp.[reply]

According to this PMID 11178284 abstract: Sliding clamp proteins are found in all organisms and are called proliferating cell nuclear antigen (PCNA) in eukaryotes and the beta clamp in prokaryotes. See also PMID 7478986 and this. The terms "DNA clamp" and "sliding clamp" are synonymous. Occasionally "beta clamp" is used as a synonym for "sliding clamp", but in most review articles that I have read, the term "beta clamp" is restricted to the prokaryotic "sliding clamp" (i.e., the beta subunit of the prokaryotic DNA polymerase III). Boghog (talk) 07:48, 18 December 2010 (UTC)[reply]

Genes VI and PCNA, and this was the delay: PCNA is first mentioned in the paragraph that begins "Initiation at the SV40 {simian virus} origin requires a product of the virus, the T antigen, to bind to the origin and initiate the process of strand separation." ... twenty five words ... "The priming reaction is unusual: it starts with Rna, like other priming reactions, but the Rna primer is extended by the Dna polymerase activity to give a short (3-4 base) Dna sequence called iDna. Replication factor C binds to the 3' end of the iDna and loads Dna polymerase delta and PCNA. (PCNA is called proliferating cell nuclear antigen for historical reasons; it acts as a processivity factor for Dna polymerase delta.)" I was about to report that Dna Pol delta is synonymous with Dna Pol III when I found this in the final section: "The two complexes of Dna polymerase delta behave in the same way as the two complexes of Dna polymerase III in the E. coli replisome. The processivity of Dna pol delta is maintained by PCNA. 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 (!), the function is likely to be identical." I defer, although the appearance of the word trimer, above, is a mystery; we were discussing simian viruses. What would you like to see happen? ~ P. S. Whereas many words starting with 'de-' have negative connotations, such as deflate, defer is an exception. Betaclamp (talk) 06:13, 21 December 2010 (UTC)[reply]

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:

prokaryotic beta clamp: 2 subunits X 3 domains/subunit = 6 domains
eukaryotic PCNA sliding clamp: 3 subunits X 2 domains/subunit = 6 domains

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)[reply]

Can't Answer yet, I'm a bit overwhelmed at the structural additions of improvements to both Dna Clamp and Beta Clamp-Sandbox. My Thanks to you for all of this is no longer overdue, i. e. Thank you. While I'm glad that the above contributed, I'd like to review 'pubmed'. Specifically, I think that I need to resolve my statement that "This intermediary is beta-clamp, a dimer in prokaryotes and a trimer in eukaryotes." with your well informed alternate. Seasons Greetings! Q. Archaea have a trimer? [see your table] ~ Betaclamp (talk) 07:19, 22 December 2010 (UTC)[reply]

Likewise, Seasons Greetings! In answer to your question, the archaea sliding clamps (and much of the associated DNA replication mechanisms) appear to be more closely related to the eukaryotic than bacterial systems. This includes the sliding clamp which is a trimer in both archaea (see for example PMID 11266590) and eukaryotes while a dimer in prokaryotes. Please also take a look a the DNA clamp article which I have extensively revised. Cheers. Boghog (talk) 08:02, 22 December 2010 (UTC)[reply]

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)[reply]

To the right, is a space filling model of PCNA that I created from scratch.

According to UniProt P12004, cyclin is an alternative name for PCNA. However I still think we need to mention PCNA as it is the accepted HUGO gene symbol and UniProt name. Concerning the beta clamp article, I suggest that we first work on it before deciding where to place it. If the length is fairly short, it could be added to the DNA_clamp#Bacterial section. If it turns out to be long, then it would justify an article of its own. Boghog (talk) 20:33, 28 December 2010 (UTC)[reply]

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)[reply]