Talk:Cytochrome P450

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[edit] What "P" in "P450" stands for

Yet more confusion! "Dale, Ritter and Rang: Pharmacology 5th Ed", pretty much *the* standard undergrad text on pharmacology gives the P as designating "Pink" as 450nm light is of a pink hue. However, P for "pigment" sounds more believable when you consider that the "P number" for chlorophylls (related to the haems of the P450s) stands for "Pigment absorbing at...". Possibily we should give all the alternative meanings and state that there is some ambiguity? Duke Of Earl 14:30, 3 March 2006 (UTC)

From the refernce reading listed (Nelson D.), it says the 'P' of Cytochrome P450 comes from 'pigment' but not 'peak'. Minor, though it may seem, should it be editted?

I want to know more . How come this article has no references/further reading? How can I trust it? 67.113.3.148 03:00, 5 May 2005 (UTC)

Thank you for your suggestion! When you feel an article needs improvement, please feel free to make whatever changes you feel are needed. Wikipedia is a wiki, so anyone can edit almost any article by simply following the Edit this page link at the top. You don't even need to log in! (Although there are some reasons why you might like to…) The Wikipedia community encourages you to be bold. Don't worry too much about making honest mistakes—they're likely to be found and corrected quickly. If you're not sure how editing works, check out how to edit a page, or use the sandbox to try out your editing skills. New contributors are always welcome. JFW | T@lk 06:20, 5 May 2005 (UTC)

If I knew the answer, I would. This is a request for more info from those who know. Like a reference into the literature is something I like, and something all articles should have, in my opinion.67.124.100.215 07:33, 9 May 2005 (UTC)

"The Human Genome Project has identified 63 human genes coding for the various cytochrome P450 enzymes." Well, what are they? Some are listed, what are the rest?67.124.100.215 07:33, 9 May 2005 (UTC)

Listen mate, Wikipedia is built by normal people like you and me. If you would like to help increase the quality of this article, you could look at other sources (there must be a list of cytochrome P450 genes somewhere on the internet) and incorporate the relevant material - in your own words - into Wikipedia. Occasionally information can be added on request, but you cannot insist on this. Wikipedia is a work in progress, and references are still lacking in a large number of articles.
Trustworthiness of Wikipedia is obviously an issue. The disclaimer is clear about this. JFW | T@lk 08:28, 9 May 2005 (UTC)
No problem, I'm not insisting on or expecting anything; I just like to encourage the wonderful contributors by letting them know we care.GangofOne 08:53, 9 May 2005 (UTC)

I think listing the human CYPs individually (eg separate lines for CYP1A1, CYP1A2, CYP1B1, etc) is not necessarily the best way of presenting them. There are not (and will not likely be) individual pages for each CYP. More to the point, it is sometimes impossible to assign individual functionality to each CYP - they tend to have overlapping specificity. I'm not sure an arragement that gives such an 'outline' of the CYPs is the correct way to go. In addition, the numbers from the family and subfamily are confusing enough, especially since a simple list gets out of sync with the names. Comments? Jed 03:45, 6 March 2006 (UTC)

[edit] Only 18 families?

Although I have no text books available to confirm this, my lecturer (and my lecture notes) seem to suggest there are in fact 21 families?

There are a great many more than 21 CYP families. At last count (Oct 2006) there were 6422 known sequences in 708 families (99 in animals). Jed 21:43, 14 November 2006 (UTC)

[edit] Serious work needed

This page needs serious work in order to remove some plain falsities and add valuable information that is now known about the enzyme family. I'll work on this article after I finish my thesis...on computational study of P450s. ju66l3r 20:00, 9 November 2006 (UTC)

Hopefully not that much that is plainly false. Plenty of info to add - to the extent that it might be useful to keep a summary paragraph/section at the top.... Jed 21:44, 14 November 2006 (UTC)

Agreed. I removed some of the blatantly weird additions (like BM3 under human p450s?) at the time. I figured if something that wrong was in there, then it's quite possible I missed even more in my haste. There are quite a few things this article could use, including comments on some of the latest research as well. ju66l3r 06:15, 15 November 2006 (UTC)

[edit] Nomenclature

I'm trying to keep the nomenclature consitent, with the official name (CYP#letter#) first and the common name following in parentheses. As the sequences proliferate it becomes useful to try to keep the nomenclature consistent. Contact David Nelson, the P450 nomenclature guy, if you have comments on the specifics of the nomenclature. Jed 21:53, 14 November 2006 (UTC)


== Title ==450 Colleagues, does anybody know why on earth this article is titled "Cytochrome P450 oxidase"? The widely accepted, if not quite correct, name of this superfamily is "cytochrome P450" (CYP for short); many people nowadays prefer to call it simply "P450" (in contrast to cytochromes, which are purely electron-transfer proteins, P450s are enzymes). It seems that this article started as "P450", then was renamed "Cytochrome P450 oxidase". It is unfortunate name, since (by analogy with cytochrome c oxidase) one can think this is the enzyme that... oxidizes cytochrome P450! Moreover, "oxidase" cannot be applied to all P450s since some of them are not classified as oxidoreductases at all. (See P450-containing systems). I suggest renaming this article back to "P450". Metalloid 01:10, 9 February 2007 (UTC)

I believe P450 may be too short of a title, but I do agree that oxidase is not reasonable because not all P450s are oxidases and more importantly the article is not about oxidases of cytochrome P450s as correctly pointed out. I would suggest Cytochrome P450 as a better title than just P450 or the current title. ju66l3r 18:49, 9 February 2007 (UTC)

I concur that Cytochrome P450 is the preferred title/enzyme name. I believe this is the overall name preferred by the Cytochrome P450 nomenclature committee. Jed 02:28, 13 February 2007 (UTC)

I've moved the article as requested. I actually merged the histories of the article and the redirect that was previously at Cytochrome P450 - the first three edits in the history contain content that was merged to the article Cytochrome P450 oxidase in the fifth edit. -GTBacchus(talk) 02:32, 15 February 2007 (UTC)
Thanks, GTBacchus. ju66l3r 07:42, 15 February 2007 (UTC)

[edit] Introduction needs work

I don't think that the "main" reaction carried out by P450's should be listed in the introductory paragraph. Many important reactions carried out do not have that stoichiometry, and while it's perhaps useful to have it listed, I feel that it should be further down the page. I'm commenting here rather than making the edits to gather opinions. Jed 15:05, 26 February 2007 (UTC)

The formula itself might be better placed in the article body and not the WP:LEAD but can you suggest alternative text that would summarize the fact that this enzyme is very notable because of the interesting chemistry performed by most of the members of the family? I wouldn't remove it without something to replace it that would still explain the highly interesting biochemistry for which P450s are known. ju66l3r 19:17, 26 February 2007 (UTC)

[edit] Merge with P450-containing_systems

I feel that P450-containing_systems should be merged in to the main P450 page. If each eletron transfer protein were to have its own page with mention of CYPs and a link that would be fine, but it doesn't make sense to separate out the information on CYP electron transport.Jed 15:05, 26 February 2007 (UTC)

It's usually not kosher to alter someone else's comments on a talk page, but your article link was not valid so I corrected it for you this one time. I also added {{merge}} tags to the two articles to help generate a greater response to your proposal. ju66l3r 19:15, 26 February 2007 (UTC)
Thanks. I didn't have any time to fix/check the link or to look up the merge tags when I posted. Jed 21:42, 28 February 2007 (UTC)
As for the merge request, it might work. I would worry about the total size of the article getting a bit big. I know, for example, that the current article (Cytochrome P450) is not really complete in terms of coverage of the topic. So, in the end, we might end up deciding to splinter it back off to the original two articles for size considerations later. That would be my only concern. Otherwise, they're certainly compatible information and so a merge wouldn't be out-of-place by any means. ju66l3r 22:41, 28 February 2007 (UTC)
Please do not merge these articles. It is better to keep them separately. Cytochromes P450 are a part of different P450-containing_systems. But even P450 family alone is huge subject (it includes many sub-articles). Biophys 01:55, 1 April 2007 (UTC)
As I think about this, here's what I see might work best. Keep both articles seperate, BUT in this article, there should probably be a section entitled "P450-containing systems" with one of the Main article: links at the top of the section and a very brief WP:LEAD-like paragraph describing the ways in which P450s are involved in greater metabolic cycles, etc. as described in the other article.
This is frequently how articles are "spun off" from an article that grows too large. In this case, it is more that two congruent articles should be brought together and cross-referenced in the same way in my opinion. ju66l3r 18:49, 1 April 2007 (UTC)
I still think that all the information from the P450-containing_systems should be on the P450 page. It just doesn't make sense to me to think about an enzyme involved in redox transformations without reference to the source of the reducing power (electrons). I also have a problem with the title "P450-containing systems," as "systems" is a vague word with lots of different meanings in different circumstances, and it behooves us to be as clear and as precise as possible. Jed 04:04, 8 April 2007 (UTC)
As a "creator" of P450-containing_systems article, I disagree completely that it should be merged with P450 page. One of reasons I did create it was exactly to differentiate between P450 protein and P450 system. Unfortunately even EC nomenclature is guilty of propagating the confusion. Check out this link: http://www.icgeb.org/p450/P450enzymes.html. The EC numbers marked with asterisks correspond to the reactions that do include NADPH and therefore have to be considered as catalysed by CPR/P450 systems, not P450s alone. As for a term "system": it may be vague but "enzyme system" is a well-established concept in enzymology. Please consult the second paragraph of http://www.chem.qmul.ac.uk/iubmb/enzyme/rules.html. Metalloid 15:26, 10 April 2007 (UTC)
OK. I stand corrected. The IUBMB rules are pretty clear. I may still include a paragraph on sources of electrons with a pointer to the systems page, if that's ok. Jed 15:47, 11 April 2007 (UTC)
I would agree to that. This is what I described above. Use the Main article: template (sorry, can't recall the name off the top of my head) at the beginning of the section and give a brief description of what that article describes and its relation to this article. ju66l3r 19:51, 12 April 2007 (UTC)
Agree. I also think similar job has to be done on NADPH:cytochrome P450 reductase (CPR) which currently is very poorly written (e.g. its Introduction is more discussion of P450s and human CPR-containing P450 system than CPR itself). Metalloid 08:35, 17 April 2007 (UTC)
Good point about the reductase article too. Maybe we should build a list of articles that shoud be touched upon in this article with relevant Main article: links going to each of the individual articles. ju66l3r 21:08, 18 April 2007 (UTC)

[edit] How many families, how many genes?

There are quite a number of human P450 families listed here that aren't mentioned by the Human Cytochrome P450 (CYP) Allele Nomenclature Committee. Are they just listing the ones with known polymorphisms?

This is even more confusing in the light of Dr Nelson's count, which differs from both ours and the Committee's (for example, we don't list 2B7 as a pseudogene, and in fact seem to be pretty spotty in our coverage of pseudogenes, and Dr. Nelson doesn't list 2C11, 2U or 2W at all, among others.).

Of course, Dr. Nelson's page seems to be about 7 years old, so that could account for some of the discrepancies.--Slashme 21:23, 4 March 2007 (UTC)

It appears that the Human Cytochrome P450 (CYP) Allele Nomenclature Committee is indeed listing ones with known polymorphisms. For example, they're missing CYP51, probably the most ancient of CYPs, which is essential to the synthesis of cholesterol. I don't believe that there are polymorphisms in CYP51. David has recently updated his human CYP list to include lots of pseudogenes, so I'll link to there. We're not exhaustive - that's his job (well, he doesn't have grants to do it, but he does get paid to be a professor). Jed 22:14, 9 March 2007 (UTC)

[edit] Are CYPs found in all life?

The intro says "found in bacteria, archaea and eukaryotes". That is all three domains of life (excluding viruses). This says that CYPs are found generally in all forms of life; are they found specifically in all known species? That would allow the introduction 71.41.210.146 18:37, 23 June 2007 (UTC)

Well, I'm not quite sure. They have been found in a huge number eukaryotes, some archaea, and most bacteria. I'm not sure whether all archaea and all bacteria have CYPs, though. I'd actually be quite surprised. And even if that were true, by saying it that way you neatly dodge the question of what you call "life", and you also avoid such picky description as "cellular life" or "membrane-bound organisms" or what not. --Slashme 08:13, 25 June 2007 (UTC)
Not all organisms have CYPs. This is particularly evident in bacteria and archaea, but there are also eukaryotes that do not have any CYPs (ie Giardia, although that's a case of a parasite presumably discarding unneeded genes). Jed 21:17, 9 July 2007 (UTC)

[edit] Human P450s

Placing this here just in case that something is missing in the article. CYP11A1; CYP11B1; CYP11B2; CYP17A1; CYP19A1; CYP1A1; CYP1A2; CYP1B1; CYP20A1; CYP21; CYP21A2; CYP24; CYP24A1; CYP26A1; CYP26B1; CYP26C1; CYP27A1; CYP27B1; CYP27C1; CYP2A13; CYP2A6; CYP2A6V2; CYP2A7; CYP2B; CYP2B6; CYP2C18; CYP2C19; CYP2C8; CYP2C9; CYP2D6; CYP2D7P1; CYP2E1; CYP2F1; CYP2J2; CYP2R1; CYP2S1; CYP2U1; CYP2W1; CYP39A1; CYP3A3; CYP3A4; CYP3A43; CYP3A5; CYP3A7; CYP46A1; CYP4A11; CYP4A22; CYP4B1; CYP4F11; CYP4F12; CYP4F2; CYP4F22; CYP4F3; CYP4F8; CYP4V2; CYP4X1; CYP4Z1; CYP4Z2P; CYP51A1; CYP7A1; CYP7B1; CYP8B1; PTGIS; TBXAS1; Biophys (talk) 03:02, 11 December 2007 (UTC)

[edit] Eukaryotic P450's

With due respect to Biophys, I reverted the 11 December edits, for the following reasons: while many eukaryotic CYPs are membrane bound, a very significant and important fraction is not, and the roles and functions of eukaryotic P450s are far far more than hydrocarbon oxidation. Jed (talk) 17:41, 8 January 2008 (UTC)

I agree and to only comment on hydrocarbon oxidation is a bit too overgeneralized. ju66l3r (talk) 17:27, 9 January 2008 (UTC)

[edit] Protein Box Bot

Is anyone familiar with Protein Box Bot? If so, would they be able to insert this in place of the Template:pfam? Jed (talk) 19:36, 18 March 2008 (UTC)