Talk:Ubiquitin

splitting the article
The article is quite long, I suggest we move the ubiquitination part to its own article.CaffeineWitcher (talk) 18:05, 18 May 2020 (UTC)

Previous discussions without headers
Question - Is there a tumor with NF-KB and Ubiquitin affected?

-

Could someone create / find a nice image of this protein? &mdash; David Remahl 20:35, 6 Oct 2004 (UTC)

Does it have the same sequence in all eukaryotes? AxelBoldt 02:04, 7 Oct 2004 (UTC)

Is it really 'ubiquitous', as its name implies? ~GMH 05:23, 17 August 2005 (UTC)
 * I believe that is where the name comes from originally. It is present pretty much everywhere in eukaryotic cells. It is probably as important (if not more important) than phosphorylation in a massive variety of cellular function. "Darwin's Phosphate" has been used to describe it by our lecturer (R.J Mayer who edited the book cited by this article...he likes it a lot). --Sinkingpie 21:09, 14 May 2006 (UTC)

Should we be using the term "ubiquitylation"? Is it not generally called "ubiquitination" at present? Jamie 17:20, 29 January 2006 (UTC)
 * I've rewritten the intro to reflect this. -- stillnotelf   is invisible  21:21, 31 March 2006 (UTC)
 * Ubiquitination is in common usage even within the scientifc literature, although ubiquitylation is strictly speaking the correct terminology -- RogerDodger 22:41, 5 April 2006 (UTC)

Limpets for ubiquitin antibody?
Why are just keyhole limpets used for making ubiquitin antibody? Links for example: [], []. --Snek01 14:19, 5 April 2006 (UTC)
 * Keyhole limpet haemocyanin is a commonly used immune stimulant - it is attached to the protein/peptide of interest and injected into an animal which then raises an antibody response against the protein.--RogerDodger 22:41, 5 April 2006 (UTC)

Ubiquitin in Archaea and the Proteasome
Should we have some mention of ubiquitin in archaebacteria? The protein is relatveily conserved from them to eukaryotes, but the article suggests that it is only important in the latter.

There also seems to be a large emphasis on the proteasome. I think that thought is generally moving away from ubiquitin being simply a signal for degradation. e.g. transcriptional regulation, DNA repair etc. (the book mentioned in further reading has a lot on this sort of stuff). --Sinkingpie 10:20, 10 May 2006 (UTC)


 * I added a mention of mono-ubiquitination to deal with this point... though did not use your examples, so you may want to add those. Gacggt 04:49, 27 May 2006 (UTC)


 * I added the prokaryotic ancestors to Ub. --Enozkan (talk) 04:52, 8 January 2010 (UTC)

VHL
VHL is a member of a complex with E3 ubiquitin ligase activity. VHL itself is not an E3 ubiquitin ligase.

Human ubiquitin sequence
The human ubiquitin sequence is:

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

This section was added by anonymous user 86.6.171.123 on December 18, 2005. Can someone verify what this is, and perhaps explain to a layman what this means, either with a wikilink or a couple of sentences to assure us that it isn't just someone pounding on their keyboard? Neil916 (Talk) 18:47, 4 January 2007 (UTC)


 * This is the amino acid sequence of the mature Ubiquitin. Each one of these letter represents one amino acid. All is legit. Here is the NCBI page for the Ubiquitin precursor that results from the translation of the human UBB (one of the few genes that code for ubiquitin) mRNA - scroll at the very bottom of it where you'll find a small section called "ORIGIN"


 * ORIGIN
 * 1 mqifvktltg ktitleveps dtienvkaki qdkegippdq qrlifagkql edgrtlsdyn
 * 61 iqkestlhlv lrlrgg mqif vktltgktit levepsdtie nvkakiqdke gippdqqrli
 * 121 fagkqledgr tlsdyniqke stlhlvlrlr gg mqifvktl tgktitleve psdtienvka
 * 181 kiqdkegipp dqqrlifagk qledgrtlsd yniqkestlh lvlrlrggc


 * This is the amino acid sequence of the ubiquitin precursor. I have colored the part that is going to be mature ubiquitine, after the precursor gets cleaved, and as you can see it is identical to the one in the article.
 * If you go to the NCBI protein page of another human gene that codes for ubiquitin - UBC - you'll find the same sequence embedded in a different precursor.


 * ORIGIN
 * 1 mqifvktltg ktitleveps dtienvkaki qdkegippdq qrlifagkql edgrtlsdyn
 * 61 iqkestlhlv lrlrggmqif vktltgktit levepsdtie nvkakiqdke gippdqqrli
 * 121 fagkqledgr tlsdyniqke stlhlvlrlr ggmqifvktl tgktitleve psdtienvka
 * 181 kiqdkegips dqqrlifagk qledgrtlsd yniqkestlh lvlrlrggmq ifvktltgkt
 * 241 itlevepsdt ienvkakiqd kegippdqqr lifagkqled grtlsdyniq kestlhlvlr
 * 301 lrgg mqifvk tltgktitle vepsdtienv kakiqdkegi ppdqqrlifa gkqledgrtl
 * 361 sdyniqkest lhlvlrlrgg mqifvktltg ktitleveps dtienvkaki qdkegippdq
 * 421 qrlifagkql edgrtlsdyn iqkestlhlv lrlrggmqif vktltgktit levepsdtie
 * 481 nvkakiqdke gippdqqrli fagkqledgr tlsdyniqke stlhlvlrlr ggmqifvktl
 * 541 tgktitleve psdtienvka kiqdkegipp dqqrlifagk qledgrtlsd yniqkestlh
 * 601 lvlrlrggmq ifvktltgkt itlevepsdt ienvkakiqd kegippdqqr lifagkqled
 * 661 grtlsdyniq kestlhlvlr lrggv


 * I hope that makes it clear for ya. -- Boris 10:31, 11 January 2007 (UTC)

Fuction of Ub..
brief note: Ub is not only for labeling of proteins destined for degradation but also for activation of many other enzymes and signal proteins (e.g. TAK1 in JAk-MyD88 Pathway or FANCD2 in RAD51-med. HR). P.S. The editor or author (or somebody else) should correct the introduction... I.S. 77.133.43.210 18:37, 14 July 2007 (UTC)

Ubiquitin B
I'm adding content from ProteinBoxBot and made a new page for Ubiquitin B. But glancing at your ubiquitin article, I get the impression there is only one gene for ubiquitin? If that's the case, feel free to merge the Ubiquitin B content and protein box into this article. Forluvoft (talk) 16:35, 17 November 2007 (UTC)

lys 46?
I added the number 46 to the K residue (I got that from lewin genes 7) but took it out as I was told today that main poly-ub site is K48, I do not want to count or search in pubmed, just for a numer. --Squidonius (talk) 00:01, 16 January 2008 (UTC)


 * Hello, K48 is the correct place for ubiquitination. Just have a look at the amino acid sequence and count for the place of the lysine, and you will see that lysine is at 48th position. —Preceding unsigned comment added by 89.244.182.188 (talk) 14:01, 29 January 2008 (UTC)

Removal of merge section tag
Hello. I've removed the merge tag from the ubiquitination section because when I clicked on the link to the article proposed to be merged in I ended up redirected here. Presume someone must have done the merge/redirect already and forgot to remove the tag.163.1.180.235 (talk) 11:07, 14 April 2008 (UTC)

Section on Crystal structure of ubiquitin aldehyde and deubiquitinating enzyme
Hi there, do we really need the image of the crystal structure of ubiquitin aldehyde and a deubiquitinating enzyme? It seems out of context, not connected with the main body of the text. If anything, this should probably be moved to an article on deubiquitinating enzymes (DUBS) —Preceding unsigned comment added by Rogerdodd (talk • contribs) 08:25, 12 September 2008 (UTC)

Cell organelle??
I would suggest that the proteasome is not an organelle. Rather it could be called a molecular machine or similar.

--Felix Tritschler (talk) 10:14, 22 February 2011 (UTC)


 * Agreed. The proteasome is not an organelle. I am changing it to a large protein complex, but further improvements (such as the suggestion "molecular machine") are welcome. Enozkan (talk) 06:31, 13 March 2011 (UTC)

Dietary Pathways to Higher UBQLN1 Brain Levels In Humans
Give the recent scientific correlation between higher UBQLN1 brain levels and lower incidence of Alzheimers disease, I'm wondering if there is any data or other science on foods that might boost Ubiquitin1 in the brain.

H.Tamahagane 20:42, 1 September 2011 (UTC) — Preceding unsigned comment added by H.Tamahagane (talk • contribs)

Orphaned references in Ubiquitin
I check pages listed in Category:Pages with incorrect ref formatting to try to fix reference errors. One of the things I do is look for content for orphaned references in wikilinked articles. I have found content for some of Ubiquitin's orphans, the problem is that I found more than one version. I can't determine which (if any) is correct for this article, so I am asking for a sentient editor to look it over and copy the correct ref content into this article.

Reference named "entrez": From UBE2O:  From UBE1DC1:  From BAG1:  From SAE1:  From HSPA14:  From Small ubiquitin-related modifier 1:  From DNAJB9:  From ATG12: </li> <li>From UBE2E1: </li> <li>From SUMO3: </li> <li>From HSPA6: </li> <li>From HERPUD1: </li> <li>From Clusterin: </li> <li>From DNAJA3: </li> <li>From UBE2E2: </li> <li>From DNAJC1: </li> <li>From UBE2C: </li> <li>From HSPA1B: </li> <li>From UBQLN2: </li> <li>From UBE2B: </li> <li>From DNAJB2: </li> <li>From DNAJC11: </li> <li>From HSPA4L: </li> <li>From DNAJA2: </li> <li>From FANCL: </li> <li>From RPS27A: </li> <li>From DNAJC7: </li> <li>From FAU (gene): </li> <li>From UBE2R2: </li> <li>From DNAJB1: </li> <li>From UHRF1: </li> <li>From DNAJA1: </li> <li>From DNAJC14: </li> <li>From Ubiquitin A-52 residue ribosomal protein fusion product 1: </li> <li>From DNAJC13: </li> <li>From DNAJB6: </li> <li>From UBE2A: </li> <li>From Histidine ammonia-lyase: </li> <li>From UBE2L3: </li> <li>From UBE2E3: </li> <li>From TMUB2: </li> <li>From Heat shock protein 47: </li> <li>From UBL5: </li> <li>From UBE2D3: </li> <li>From UBQLN1: </li> <li>From DNAJB4: </li> <li>From UBE2G1: </li> <li>From Ubiquitin D: </li> <li>From CUL7: </li> <li>From SAE2: </li> <li>From UBE2V2: </li> <li>From SUMO2: </li> <li>From HSPA1A: </li> <li>From GroES: </li> <li>From UBE2D1: </li> <li>From HSPA4: </li> <li>From UBE2L6: </li> <li>From UBE2M: </li> <li>From UBR1: </li> <li>From UBE2V1: </li> <li>From UIMC1: </li> <li>From UHRF2: </li> <li>From OASL: </li> <li>From UBL4A: </li> <li>From SUMO4: </li> <li>From SF3A1: </li> <li>From SMN1: </li> <li>From UFM1: </li> <li>From HSPA1L: </li> <li>From HSPA9: </li> <li>From UBE1: </li> <li>From HSPA2: </li> <li>From Ubiquitin C: </li> <li>From HLA-B associated transcript 3: </li> <li>From RAD23A: </li> <li>From DNAJC10: </li> <li>From CYLD (gene): </li> <li>From ATG7: </li> <li>From UBE1C: </li> <li>From UBE2N: </li> <li>From RAD23B: </li> <li>From TRAP1: </li> <li>From CDC34: </li> <li>From DNAJC3: </li> <li>From UBE1L2: </li> <li>From DNAJB11: </li> <li>From UBE2D2: </li> <li>From DNAJC6: </li> <li>From UBE2G2: </li> <li>From USP6: </li> <li>From BIRC6: </li> <li>From HSPA8: </li> <li>From DNAJC19: </li> <li>From APPBP1: </li> <li>From DNAJC5: </li> <li>From SMN2: </li> <li>From UBE2J1: </li> <li>From UBE2H: </li> <li>From UBE1L: </li> </ul>

I apologize if any of the above are effectively identical; I am just a simple computer program, so I can't determine whether minor differences are significant or not. AnomieBOT ⚡ 01:36, 2 September 2011 (UTC)

Disease associations
I removed the following from the section on disease associations, because there is no explanation of how this relates to the ubiquitin pathway:


 * The gene disrupted in Liddle's Syndrome results in disregulation of an epithelial Na+ channel (ENaC) and causes hypertension.

If this legitimately is connected with the ubiquitin pathway, please add it back to article, along with an explanation of what the link is.

139.173.54.11 (talk) 19:00, 13 January 2012 (UTC)

Scheme of isopeptide bond
Hello.

It would be really helpful if you could add a scheme (preferably with atom letters not just lines) of isopeptide bond between Lys48 and Gly76.

Thank you very much. Schjora (talk) 21:10, 6 February 2013 (UTC)

Split of variety and function
I have added info and made some major layout changes. I have split the variety+functions section because there was some mention of certain linkages on specific proteins in the monoubiquitin section but not in the lysine chains. The idea was that the types of chains are explained in the variety section and then the specific modifications of proteins could be explained in the functions section with an explanation of the cellular functions that they affect. This will hopefully encourage the expansion of this page because additions to each section should be easier. Also the list of functions that is already on the page is exact copy from here. If the functions section is expanded with journal articles then this can eventually be removed. If there are any issues with anything that I have changed then please let me know. Simon Caulton (talk) 21:41, 22 July 2013 (UTC)

Summary and Intro to tools & techniques
Ubiquitin System: The Next Class of Drug Targets? has interesting info (eg. " ~4,600 human proteins are modified at more than 23,000 sites", "the UPS involves two E1s, ~ 38 E2s, and more than 600 E3 ligases, as well as ~ 100 deubiquitylases (DUBs).") (and context, eg comparison with the extracellular glycosylation processes). - Rod57 (talk) 11:14, 3 March 2017 (UTC)

De-jargonfy and make readable
This article is probably the hardest to read and jargon filled biology article I have come across. It's clear many edits may have been made by those passionate to the field, unfortuantely putting details before significance. It would really be a service if someone could go though with a fine-toothed comb and achieve this. Musa acuminata (talk) 18:42, 18 May 2019 (UTC)