Talk:DNA polymerase II

Peer review and responses during the educational assignment in Winter 2015

As part of this class, peer review by three different colleagues was done in order to generate the best article possible. It was suggested by our Chemistry Librarian to add these reviews.

From NA (student without known username at this time)

Group1 Peer Review Section1: I think the overall length of is appropriate for wiki page. Some information about pol II does exist in the DNA polymerase page. Group2 does well in expansion of the detail about DNA pol II further. The page include critical information about pol II and are well-categorized. However, you might want to create a link to DNA polymerase site as well as exonuclease and pol III site. Section2: Group2 does well to bring up the main concepts about pol II. However, some sections seem to be a bit short and could have been better with some more detail information. Comment on each section will be provided later on. Some sections such as general structure and crystal structure should be combined together unless there is some critically different information to point out. Personally, I’m not entirely sure whether you need to point out the angle and length in crystal structure part. It might be clearer with the figure, but as mention later on about conformational change, I wonder whether this information is important or not. Mechanism part seems a bit too short for me in relative to how important this part should be. The figure included in outline look pretty nice and well-fit to illustrate the explanation. Section3: Group2 provides well-diverse set of reference including review article and online article. However, I don’t think it’s appropriate to include another wiki page as reference. Overall comment Group2 provides important information about pol II in a well-categorized format. The explanation is concise and informative. However, some section could be expanded to make it better while some section could be collapsed. Overall, the work done by group2 provide significant improvement to DNA pol II wiki page.  Addition comment on each section 1 History -Do you have reference for rolf knippers? -You didn’t mention how pol II got the name pol II as plan in the outline. I think you can extend this part in more detail -You mention about crystallization of pol II by Anderson et al. separately from “myriad of studies during the past few year”. You might want to elaborate on this more if you feel it is a very important step in term of study of pol II. -Overall, I feel the language is kind of disconnected in this paragraph. This might be automatically fixed when you give some more detail expansion as mention earlier. 2 General structure 2.1 Structure and function - In my opinion, I don’t think the last sentence you mention about expression level and comparison to pol III belong to this sub-section. - Do you have any reference for the information? 2.2 Crystallography - I’m not sure how significant this part is. Can it be combined with general structure? Do you even need to include this section in the first place? 3 Mechanism - The information in this part is somewhat lacking. I think you can elaborate more detail here, for example, describing which domain of pol II bind to which location and explain role of each domain of pol II during the mechanism.

From UMcrc14, Section 1

The objectives listed in the outline were general, but appropriate for Wikipedia. I did not find much information about DNA polymerase II on other websites besides digging through literature articles—which there was not much there either. After a brief search through SciFinder, I did not even find a review article on this topic. Kudos for picking this topic without much information to go off of! This Wikipedia article will be a good contribution for people who want a quick idea of what DNA pol II is or does because there is not really a site that has the information all in one place. I think the length is appropriate, but some sections should be expanded upon to explain jargon.

Section 2

Much of the information that I read in the article I felt was repeated throughout at least a couple times (excluding the introduction). I would suggest reading through the entire site as a group and seeing which pieces of information are most pertinent to a section, and if it is pertinent to both, keep it, but if not condense. The only important concept that is missing is the “Health Impacts” section that was listed in your outline, I think this would be something the general audience would be interested in if there is relevant information. There is also a bit of jargon within the text that was not explained, for example, the crystallography section. I would suggest linking “tricky” words to other Wikipedia pages and also not using acronyms unless you have it spelled out somewhere previously on the page. I also noticed quite a few grammatical and some spelling errors, be sure to do a thorough proofread of the site.

Images

The addition of the crystal structure to the page is a good touch. However, that is the only picture on the page, so far anyways. I really liked the pictures you had in your outline! I think it would be advantageous to add those maybe once you adapt them to be your own. It also might be useful to add pictures explaining the exonuclease activity to perform repair as that seems to be one of DNA pol II’s major functions.

Section 3

There are citations that appear more than once in the references section, so you definitely need to condense that. As I said earlier, I couldn’t find many papers on DNA Pol II, so I think your section has a good mix based on your options to choose from.

Overall comments

Overall, I think the site provides a better understanding of the role that DNA Pol II has in replication, even though it is still being studied. My major recommendations would be to proofread for small errors (such as capitalizations, italicizations, spelling, etc.), add more images, add links to other pages (either within Wikipedia or to outside cites), and to condense the references section. Also be careful of words that may have an obvious meaning to us as graduate students, but may be foreign to the general reader—definitely use them, but either explain briefly in your text, or link to another page if there is one.

From jglundgr, The goals are clear and appropriate for the first section. There were only a few minor changes I would propose. When E. coli is talked about in the history section the "c" should be lowercase. Replication is misspelled. Maybe a link explaining who Rolf Knippers is would make the sentence a little clearer. In the last sentence the "al" should be lower case. There is a good summary of the history and the general function of DNA Pol II. Had to really try to find something wrong with the first section. Looks good!

In the general structure paragraph, the only thing I might change is the wording of the last sentence. The general structure paragraph gives a good overview of the structure of DNA Pol II in a clear and concise way. The first crystallography sentence might be worded more clearly. I would just turn it into two sentences to make the sentence flow better. Also, it isn't clear what the table underneath the crystallography paragraph represents. In the Confirmed Primary Cellular Function section, the first paragraph talks about DNA Pol III being involved with DNA replication, then the next sentence talks about DNA Pol II not being involved with chromosome replication. Perhaps keep it consistent as to avoid possible confusion. The second paragraph needs a comma in the last sentence. In the proposed activity section the first sentence could be worded more clearly. The mechanism is clear and the cellular function is clear as well. I like how the relationship between DNA Pol II and DNA Pol III and IV is addressed. The regulation paragraph gives good information for how this enzyme is regulated. Overall, not too much to change in this section either.

As far as the images go, it seems like this group will add some of the pictures later. The pictures in the outline help with the overall understanding of the process of DNA Pol II. Gives a good visual representation of the processes explained in this article.

The reference seems to be pretty good as well. There is a decent mix of primary literature as well as websites and even other Wikipedia articles. I think the references are diverse and really help explain the information well.

I really had to go out of my way to find things that I would change for this Wikipedia article. All the changes I would do are very minor. This article is very clear and explains the main points of how DNA Pol II operates. I feel that someone with a small science background could learn easily from this site. It looks like you guys are off to a good start. Overall good job!

The changes that we have made are reflected in what is now the DNA Pol II page. BiochemEnthusiast (talk) 07:01, 20 February 2015 (UTC)

First Draft

In order to understand what the above critiques were of, this is the first draft that our group submitted.

First draft

DNA polymerase II Identifiers Organism Escherichia coli (str. K-12 substr. MG1655) Symbol polB Entrez 944779 PDB 3K5M RefSeq (Prot) NP_414602.1 UniProt P21189 Other data EC number 2.7.7.7 Chromosome genome: 0.06 - 0.07 Mb Search for Structures Swiss-model Domains InterPro This article is about the DNA Polymerase. For the RNA Polymerase, see RNA polymerase II DNA polymerase II (also known as DNA Pol II or Pol II) is a prokaryotic DNA-Dependent DNA polymerase encoded by the PolB gene. It is an 89.9-kDa protein and is a member of the B family of DNA polymerases. It was originally discovered in 1969 by De Lucia and Cairns and named and characterized in the years following. The in vivo functionality of Pol II is under debate, yet consensus shows that Pol II is primarily involved as a backup enzyme in prokaryotic DNA replication. The enzyme has 5’->3’ DNA synthesis capability as well as 3’->5’ exonuclease proofreading activity. DNA Pol II interacts with multiple binding partners common with DNA Pol III in order to enhance its fidelity and processivity. History The isolation of a strain of E. Coli deficient in DNA polymerase I (termed Pol A1-) by De Lucia and Cairns in 1969 prompted a range of studies. As characterized, the strain retained some DNA replication activity. The isolation and characterization of the polymerase believed to be involved in DNA replicatioin in the absence of the original polymerase followed by rolf knippers. In vitro activity was elucidated through a myriad of studies over the following years. The protein was crystallized by Anderson et. Al in 1994, but scientists still debate today as to its function. Structure and Function General Structure DNA Pol II is an 89.9 kD protein, comprised of 783 amino acids, that is encoded by the polB (dinA) gene. A globular protein, DNA Pol II functions as a monomer, whereas many other polymerases will form complexes. There are three main sections of this monomer colloquially referred to as the palm, fingers, and thumb. This “hand” closes around a strand of DNA. The palm of the complex contains three catalytic residues that will coordinate with two divalent metal ions in order to function. Normal cell levels of DNA Pol II are around 30-50 copies per cells, which is a high quantity in comparison with the number of Pol III HE molecules in a cell which is five times fewer. An example of the Group B polymerase with marked palm, fingers, and thumb sections. An example of the Group B polymerase with marked palm, fingers, and thumb sections. Crystallography DNA Pol II was first crystallized in 1994 by Anderson et. al. In 2009, the structure was crystallized with DNA and a deoxynucleotide, dCTP in the following data, but dATP, dTTP, and dGTP were all also crystallized, by Wang et al. This crystal has great resolution to 1.92 angstroms. Its space group is P212121. Length (Angstroms) Angles (Degrees) a = 80.73 α = 90.00 b = 100.66 β = 90.00 c = 126.03 γ = 90.00 Structural Similarity to Other Group B Polymerases Most of the polymerases have been grouped into families based on similar structure and function. DNA Pol II falls into the Group B along with human DNA Pol α, δ, ϵ, and ζ. These are all homologs of RB69, 9°N-7, and Tgo. The other members of group B do have at least one other subunit which makes the DNA Pol II unique. Primary Cellular Function Confirmed Polymerases all are involved with DNA replication in some capacity. DNA replication is a vital aspect of a cell’s proliferation. Without replicating its DNA, a cell cannot divide and share its genetic information to progeny. In prokaryotes, like Escherichia coli (E. coli), DNA Pol III is the major polymerase involved with DNA replication. While DNA Pol II is not a major factor in chromosome replication, it does has other roles to fill. There are many different ways that DNA can be damaged, from UV damage to oxidation, so it is logical that there are different types of polymerases to fix these damages. One important role that DNA Pol II is the major polymerase for is the repairing of inter-strand cross-links. Interstrand cross links are caused by chemicals such as nitrogen mustard and psoralen which create cytotoxic lesions. Repairing these lesions is difficult because both DNA strands have been damaged by the chemical agent and thus the genetic information on both strands is incorrect. The exact mechanism of how these Interstrand cross-links are fixed is still being researched but it is known that Pol II is highly involved. DNA Pol II does participate in DNA replication, however, as DNA Pol III works quickly and processes high numbers of nucleotides per binding event, whereas DNA Pol II is much slower. This enzyme does have an associated 3’ → 5’ exonuclease activity along with primase activity. The important quality of DNA Pol II is that it is a high fidelity enzyme with an error rate of substitution: ≤0.2*10-5 and -1 deletions: ≤ 0.1*10-5. DNA Pol II can proofread and process mismatches caused by the Pol III HE errors which demonstrates that DNA Pol II is an important enzyme to the cell. Banach-Orlowska et al. showed that DNA Pol II is involved with replication but it is strand dependent and preferentially replicates the lagging strand. A proposed mechanism from Banach-Orlowska et al. suggests that when DNA Pol III stalls or becomes non-functional, then DNA Pol II is able to be specifically recruited to the replication point and continue replication. Proposed Activity DNA Pol II is not the most studied polymerase so there are many proposed functions of this enzyme which are all likely functions but are ultimately unconfirmed. These are: repair of DNA damaged by UV irradiation, replication restart in UV-irradiated E. coli, adaptive mutagenesis, and long term survival. (Banach-Orlowska) Mehcanism During DNA replication, base pairs are subject to be damaged or misplaced in the sequence and this damaged sequence causes replication to be stalled. DNA Polymerase II catalyzes the repair of nucleotide base pairs so that replication can overcome these obstacles. The N-terminal domain of DNA Pol II is responsible for catalytic activity of the enzyme. There are at least two sites in the N-terminal domain of DNA Pol II that recognize single-stranded DNA. One site(s) is responsible for recruiting DNA Pol II to single-stranded DNA and another site(s) is responsible for the dissociation of DNA Pol II from single-stranded DNA. Kinetic Mechanism Up binding of substrate, DNA Pol II bind nucleoside triphosphate to maintain hydrogen bonded structure of DNA. The correct dNTP is then bound, at this point the complex undergoes conformational changes of subdomains and side-chains. These conformational changes allow the rate of repair synthesis to be fast. Eukaryotic versus Prokaryotic Prokaryotic Functional Relationship to DNA Polymerase III and IV DNA Polymerase II is a member of the polymerase B family and supports Polymerase III in DNA replication moving from the 3’ end to the 5’ end. In the case when Polymerase III stalls during a replication error, Polymerase II can interrupt and excise the mismatched bases. Polymerase II has a much higher fidelity factor than Polymerase III, meaning that it is much less likely to create mispairings, which helps it to act as a proofreader for Polymerase III. Without Polymerase II’s proofreading step, Polymerase III would extend the mispairings and thus create a mutation. In addition to protecting from mutations that could be caused by Polymerase III, Polymerase II functions to protect against mutations caused by Polymerase IV. Polymerase IV is much more error prone than Polymerase II but also functions to repair mismatched base pairings starting from the 3’ end. Polymerase II protects the 3’ end from Polymerase IV and blocks it from acting. This protection will prevent the formation of mutations while the Polymerase II is functioning normally. If the Polymerase II is knocked out by a mutation or disabled by other factors, Polymerase IV will take its place to fix the mispaired bases. Eukaryotic Function and Relation to Eukaryotic Polymerases While Polymerase II will not function naturally in conjunction with the eukaryotic members of Family B, it does share similar structural and functional motifs. The members of Family B include Polymerase α, ε, ζ, and δ. These polymerases all function to proofread the newly synthesized DNA in the 3’ to 5’ direction. These polymerases are capable of synthesizing DNA on both the leading and lagging strands. This class of polymerase tends to be very accurate which allows them to correct any mispairings that occur during DNA synthesis. Regulation DNA Polymerase II is naturally abundant in the cell, which usually amounts to five times greater than the amount of Polymerase III. This greater abundance allows Polymerase II to overpower Polymerase III in the case of mispairings. This amount can be increased upon the inducement of the SOS response, which upregulates the polB gene so the amount of Polymerase II increases to about seven fold greater. Although Polymerase II can work on both strands, it has been shown to prefer the lagging strand versus the leading strand. See also DNA replication References Category:DNA replication Category:EC 2.7.7 Category:Enzymes {{Transferase-stub}}

BiochemEnthusiast (talk) 07:10, 20 February 2015 (UTC)

Note to Post

I am working on this article as a part of my educational assignment from January to February, 2015. We plan to expand this stub and add sections such as history, structure and function, mechanisms, and comparisons between the different kinds of polymerases. BiochemEnthusiast (talk) 06:40, 20 February 2015 (UTC)

Reinitiation

Does the ability to reiniate mean, that in contrast to polIII it is possible for polII to start replication without primer? -- 132.187.246.71 (talk) 08:56, 15 September 2009 (UTC)

Characterization as a "prokaryotic DNA polymerase"

I believe the double-stranded DNA virus family Iridiviridae also has a gene coding for DNA polymerase II. If my information is correct than the article should indicate that this enzyme appears in both viruses and prokaryotes. Other than this apparent omission, I found the article quite helpful to an amateur such as myself.Ray Glock-Grueneich (talk) 07:01, 13 January 2014 (UTC)Ray Glock-Grueneich

about mechanism part

I think the mechanism part is the most important section in the work of poly II, so it is important to add more details such as background for this process.moreover, the article needs to add more images of the mechanism section this will illustrate the process of the DNA Replication. however, the references that used in the article are good and reliable, also the writer used good writing structure--Albahrani Batool (talk) 21:36, 28 January 2017 (UTC)