Talk:Function of moonlighting protein glutamate racemase

Merger proposal
The majority of this article exists on the Glutamate racemase page verbatim; it does not add any new information and should be deleted. Additionally, the errors it contains in citations are fixed on the Glutamate racemase article already. Pleiotrope (talk) 17:21, 1 April 2011 (UTC)

Team 10
Summary: This article talks about the properties that make glutamate racemase a moonlighting protein. The protein’s primarily role (bacterial wall synthesis) and minor role (gyrase inhibition) are described in detail. Furthermore, the article shows that both functions are not related and that their active sites seem to be independent. The main points discussed in this article are stated in the abstract which gives the reader from the start a good sense of what is to be expected in terms of content. Overall it is a well-written, properly structured, and concise article. The information contained in the article was carefully selected, researched, and explained. Major concerns: You might need to clarify the fragment “The minor functions of these unique enzymes are called moonlighting functions, in which a protein can have a second function not dependent upon the main function. The two functions of moonlighting proteins are found in a single polypeptide chain” included in the Background section. This makes the reader think that moonlighting proteins can only have two functions (a main function and a minor function). That is the case for Glutamate racemase, but not for all moonlighting proteins (GAPDH has several roles for example). Minor concerns: We think you should consider revising your citations’ format. It might be more appropriate to follow Wikipedia’s format for citations which consists of numbers inside brackets [ ] referring to the details of the citation listed at the end of your article. We believe that the method that you used (parenthesis with the article’s author and year) is less efficient in linking the text to its source, and also tends to distract the reader. This is the link that explains how to format the citations: http://en.wikipedia.org/wiki/Wikipedia:Citing_sources. It might be helpful to add figures to illustrate some of the concepts and mechanisms described in the article such as bacterial wall synthesis and gyrase inhibition.Saezcab17 (talk) 16:26, 12 April 2011 (UTC)

The style of the "Background" section seems to be more of a the style associated with an English paper, introducing a topic. Background generally gives a basis of knowledge for the reader to understand the topics that follow. While the information is good within the background section, some of the language, such as "the active site utilized by Murl will be explored..." sounds out of place. Santosze (talk) 21:38, 12 April 2011 (UTC)

Also, in the Bacterial Wall Synthesis section, the sentence "This deprotonation forms an anion and after that there is a reprotonation of the substrate". is very awkwardly worded. It would help the reader understand the process being described if it was reworded in a more clear way. Santosze (talk) 21:38, 12 April 2011 (UTC)

This is purely cosmetic, but in the Relationship to the active site section, you used the term kcat, it would look more professional if you either used a symbol for Kcat or if you wrote cat in subscript to emulate the actual symbol. Santosze (talk) 21:38, 12 April 2011 (UTC)

The sources cited by the text are accurate to the information cited and are appropriately cited. [The left column of sources was examined for accuracy.] As noted above, however, one might consider using the wikipedia format for citations. Wi lk14 (talk) 23:26, 12 April 2011 (UTC)

Group 3
Summary of "Function of Moonlighting protein Glutamate Racemase"

The functions of the moonlighting protein glutamate racemase, also known as Murl, include synthesis of bacterial cell walls and gyrase inhibition. For bacterial wall synthesis, Murl interconverts glutamate enantiomers into D-glutamate in a co-factor process in which the enzyme undergoes deprotonation and then reprononation to form an anion and achieve a conformational change in its domain. This change in domain causes the cysteine residues on either side of the substrate to superimpose at equal positions. The symmetric nature of the domains reveals that this process evolved from gene replication.

For gyrase inhibition, Murl reduces activity of DNA gyrase by preventing gyrase from binding to the DNA. Reduction in the production of DNA strands causes existing DNA to become supercoiled, which in turn prevents the reaction that causes the strands to uncoil into RNA. As there is no significant correlation between the concentrations of racemization substrate on gyrase inhibition and because each function is processed on separate active sites, glutamate racemase is a moonlighting protein, or a protein that has more than one function.

Abstract Comments

Do not use long quoted sections in your article. You do not need to directly quote what Murl is; it is the topic of your article so you should be able to summarize what it is in your own words.

You need to use footnotes, not in-text citations.

Voice: This is not a persuasive academic paper, it is an informative article. As such, don't say "will be explored to determine" or “will be studied”

The abstract is meant to be a general overview of the topic with a little background, the headings in the article make it clear what you will be discussing.

Do not label the abstract section “abstract” rather merge it with the background section below to make it the introductory portion of your article, which should be placed above the table of contents, as per Wikipedia formatting.

Background Comments

There is a LOT of repetition here with respect to the abstract. You do not need both an abstract and a background section on Wikipedia. Take out this whole section, and merge whatever isn't repeated with the abstract.

You need to clarify what you mean in the portion where you mention that “proteins that are mulitfunctional are not included...” It is not clear.

Overall Voice: Again, you do not need to lay out what you're going to talk about. This is not a normal academic paper.

Your topic is specific to Murl, you do not need to give too much information on what moonlighting proteins are in general, that is the subject of a different article.

Bacterial Wall Synthesis Comments

This is the third time you have introduced what Murl is, this is highly repetitive and unnecessary.

You also repeat what Murl’s function is again, please proofread the whole article for your next submission.

“Inter conversion” should be replaced with “interconversion”.

You already say it converts L-glutamate to D-glutamate multiple times, don't repeat yourself within the same section.

What is an allosteric site? Make it a link to another wikipedia article, or if one does not exist explain.

What is the significance of being cofactor independent?

“...meaning it can proceed without needing an additional source...” What is the additional source? An enzyme?

Replace “‘this enzyme’ involves a two step process” with “murl”.

First there is a deproteinization of the substrate, "which forms an anion.." Merge these two sentences.

Include a picture of the deproteinization/the conformational changes/superimposition to clarify those processes for the reader.

Expand on the evolution of the protein from gene duplication. It's not relevant to this section though so if it is important information put it elsewhere.

Expand on the applications of Murl and make it its own section.

Gyrase Inhibition Comments

Break this section into multiple paragraphs, it’s too long.

You prove that Murl is a moonlighting protein yet again at the end of this section; this is unnecessary and repetitive.

What is the significance of the ability of the mutated Murl being able to perform its gyrase inhibition function?

If you were expanding upon an article, you should have done so not by eliminating the original content, but actually expanding upon it. You are missing information from the Gyrase Inhibition section of the wikipedia article “Glutamate Racemase”.

Relationship Between Functions Comments

Include which active site specifically carries out bacterial wall synthesis and gyrase inhibition.

Avoid using “this” in the beginning of a sentence; indicate clearly the particular subject that is being referred to.

Combine the first and second experiment into one sentence because they both lead to the same conclusion: that there is no correlation between bacterial wall synthesis and gyrase inhibition.

The function of Murl, the topic of your article, is not to be a moonlighting protein, so do not keep reaffirming this conclusion. This is the third or fourth time you have done so. It is a moonlighting protein, but this is not its function.

Relationship to Active Site Comments

Discuss the meaning and why the active site is used to undergo racemization before analyzing whether or not the same active site is used for moonlighting function.

Replace “‘it employs two active site cysteine residues in catalysis’ as acid/base catalysts” with “it employs two active site cysteine residues as acid/base catalysts”

Do not use the phrase “This paragraph aims to determine…” Just say what you need to say and it will become self-evident.

Do not end your article with a quote.

References

The following three sources were checked and found to be valid:

Glavas S, Tanner ME (May 2001). "Active site residues of glutamate racemase". Biochemistry 40 (21): 6199–204. doi:10.1021/bi002703z.

Sengupta S, Shah M, Nagaraja V (2006). "Glutamate racemase from Mycobacterium tuberculosis inhibits DNA gyrase by affecting its DNA-binding". Nucleic Acids Res. 34 (19): 5567–76. doi:10.1093/nar/gkl704. PMC 1635304. . http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1635304.

Lundqvist T, Fisher SL, Kern G, Folmer RH, Xue Y, Newton DT, Keating TA, Alm RA, de Jonge BL (June 2007). "Exploitation of structural and regulatory diversity in glutamate racemases". Nature 447 (7146): 817–22. doi:10.1038/nature05689. .

Reference Comments

All of the included citations were already listed in an existing wikipedia article entitled “Glutamate Racemase.”  The source labeled number 10 on this wikipedia page (below) was not included.

Ashiuchi M, Kuwana E, Komatsu K, Soda K, Misono H (June 2003). "Differences in effects on DNA gyrase activity between two glutamate racemases of Bacillus subtilis, the poly-gamma-glutamate synthesis-linking Glr enzyme and the YrpC (MurI) isozyme". FEMS Microbiol. Lett. 223 (2): 221–5..

There are no citations independent of the original Wikipedia citations. Go and conduct original resource with new sources.

Format all citations using the proper Wikipedia format of footnotes, not in-text citations.

Overall Comments

Not much original research was actually conducted here, considering the fact that there is already a wikipedia article on glutamate racemase. Your topic is fairly limited, and to do the proper amount of independent work you may need to expand upon your topic, or at least add a new focus or new dimensions to your article. If these are indeed the two functions of Murl, then you have covered all of the essential points on your topic as it is currently.

Ehylton (talk) 22:28, 13 April 2011 (UTC)

—Preceding unsigned comment added by 129.2.129.147 (talk) 22:18, 13 April 2011 (UTC)