Talk:Ubiquitin
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splitting the article
[edit]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
[edit]Question - Is there a tumor with NF-KB and Ubiquitin affected?
Could someone create / find a nice image of this protein? — 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?
[edit]Why are just keyhole limpets used for making ubiquitin antibody? Links for example: [[1]], [[2]]. --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
[edit]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
[edit]VHL is a member of a complex with E3 ubiquitin ligase activity. VHL itself is not an E3 ubiquitin ligase.
Human ubiquitin sequence
[edit]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 lrlrggmqif vktltgktit levepsdtie nvkakiqdke gippdqqrli
- 121 fagkqledgr tlsdyniqke stlhlvlrlr ggmqifvktl 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 lrggmqifvk 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..
[edit]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
[edit]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?
[edit]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
[edit]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
[edit]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??
[edit]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
[edit]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)
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: "Entrez Gene: UBE2O ubiquitin-conjugating enzyme E2O".
- From UBE1DC1: "Entrez Gene: UBE1DC1 ubiquitin-activating enzyme E1-domain containing 1".
- From BAG1: "Entrez Gene: BAG1 BCL2-associated athanogene".
- From SAE1: "Entrez Gene: SAE1 SUMO1 activating enzyme subunit 1".
- From HSPA14: "Entrez Gene: HSPA14 heat shock 70kDa protein 14".
- From Small ubiquitin-related modifier 1: "Entrez Gene: SUMO1 SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae)".
- From DNAJB9: "Entrez Gene: DNAJB9 DnaJ (Hsp40) homolog, subfamily B, member 9".
- From ATG12: "Entrez Gene: ATG12 ATG12 autophagy related 12 homolog (S. cerevisiae)".
- From UBE2E1: "Entrez Gene: UBE2E1 ubiquitin-conjugating enzyme E2E 1 (UBC4/5 homolog, yeast)".
- From SUMO3: "Entrez Gene: SUMO3 SMT3 suppressor of mif two 3 homolog 3 (S. cerevisiae)".
- From HSPA6: "Entrez Gene: HSPA6 heat shock 70kDa protein 6 (HSP70B')".
- From HERPUD1: "Entrez Gene: HERPUD1 homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1".
- From Clusterin: "Entrez Gene: clusterin".
- From DNAJA3: "Entrez Gene: DNAJA3 DnaJ (Hsp40) homolog, subfamily A, member 3".
- From UBE2E2: "Entrez Gene: UBE2E2 ubiquitin-conjugating enzyme E2E 2 (UBC4/5 homolog, yeast)".
- From DNAJC1: "Entrez Gene: DNAJC1 DnaJ (Hsp40) homolog, subfamily C, member 1".
- From UBE2C: "Entrez Gene: UBE2C ubiquitin-conjugating enzyme E2C".
- From HSPA1B: "Entrez Gene: HSPA1A heat shock 70kDa protein 1B".
- From UBQLN2: "Entrez Gene: UBQLN2 ubiquilin 2".
- From UBE2B: "Entrez Gene: UBE2B ubiquitin-conjugating enzyme E2B (RAD6 homolog)".
- From DNAJB2: "Entrez Gene: DNAJB2 DnaJ (Hsp40) homolog, subfamily B, member 2".
- From DNAJC11: "Entrez Gene: DNAJC11 DnaJ (Hsp40) homolog, subfamily C, member 11".
- From HSPA4L: "Entrez Gene: HSPA4L heat shock 70kDa protein 4-like".
- From DNAJA2: "Entrez Gene: DNAJA2 DnaJ (Hsp40) homolog, subfamily A, member 2".
- From FANCL: "Entrez Gene: FANCL Fanconi anemia, complementation group L".
- From RPS27A: "Entrez Gene: RPS27A ribosomal protein S27a".
- From DNAJC7: "Entrez Gene: DNAJC7 DnaJ (Hsp40) homolog, subfamily C, member 7".
- From FAU (gene): "Entrez Gene: FAU Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30".
- From UBE2R2: "Entrez Gene: UBE2R2 ubiquitin-conjugating enzyme E2R 2".
- From DNAJB1: "Entrez Gene: DNAJB1 DnaJ (Hsp40) homolog, subfamily B, member 1".
- From UHRF1: "Entrez Gene: UHRF1 ubiquitin-like, containing PHD and RING finger domains, 1".
- From DNAJA1: "Entrez Gene: DNAJA1 DnaJ (Hsp40) homolog, subfamily A, member 1".
- From DNAJC14: "Entrez Gene: DNAJC14 DnaJ (Hsp40) homolog, subfamily C, member 14".
- From Ubiquitin A-52 residue ribosomal protein fusion product 1: "Entrez Gene: UBA52 ubiquitin A-52 residue ribosomal protein fusion product 1".
- From DNAJC13: "Entrez Gene: DNAJC13 DnaJ (Hsp40) homolog, subfamily C, member 13".
- From DNAJB6: "Entrez Gene: DNAJB6 DnaJ (Hsp40) homolog, subfamily B, member 6".
- From UBE2A: "Entrez Gene: UBE2A ubiquitin-conjugating enzyme E2A (RAD6 homolog)".
- From Histidine ammonia-lyase: "Entrez Gene: histidine ammonia-lyase".
- From UBE2L3: "Entrez Gene: UBE2L3 ubiquitin-conjugating enzyme E2L 3".
- From UBE2E3: "Entrez Gene: UBE2E3 ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast)".
- From TMUB2: "Entrez Gene: TMUB2 transmembrane and ubiquitin-like domain containing 2".
- From Heat shock protein 47: "Entrez Gene: SERPINH1 serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)".
- From UBL5: "Entrez Gene: UBL5 ubiquitin-like 5".
- From UBE2D3: "Entrez Gene: UBE2D3 ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast)".
- From UBQLN1: "Entrez Gene: UBQLN1 ubiquilin 1".
- From DNAJB4: "Entrez Gene: DNAJB4 DnaJ (Hsp40) homolog, subfamily B, member 4".
- From UBE2G1: "Entrez Gene: UBE2G1 ubiquitin-conjugating enzyme E2G 1 (UBC7 homolog, yeast)".
- From Ubiquitin D: "Entrez Gene: UBD ubiquitin D".
- From CUL7: "Entrez Gene: CUL7 cullin 7".
- From SAE2: "Entrez Gene: SAE2 SUMO1 activating enzyme subunit 2".
- From UBE2V2: "Entrez Gene: UBE2V2 ubiquitin-conjugating enzyme E2 variant 2".
- From SUMO2: "Entrez Gene: SUMO2 SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae)".
- From HSPA1A: "Entrez Gene: HSPA1A heat shock 70kDa protein 1A".
- From GroES: "Entrez Gene: HSPE1 heat shock 10kDa protein 1 (chaperonin 10)".
- From UBE2D1: "Entrez Gene: UBE2D1 ubiquitin-conjugating enzyme E2D 1 (UBC4/5 homolog, yeast)".
- From HSPA4: "Entrez Gene: HSPA4 heat shock 70kDa protein 4".
- From UBE2L6: "Entrez Gene: UBE2L6 ubiquitin-conjugating enzyme E2L 6".
- From UBE2M: "Entrez Gene: UBE2M ubiquitin-conjugating enzyme E2M (UBC12 homolog, yeast)".
- From UBR1: "Entrez Gene: UBR1 ubiquitin protein ligase E3 component n-recognin 1".
- From UBE2V1: "Entrez Gene: UBE2V1 ubiquitin-conjugating enzyme E2 variant 1".
- From UIMC1: "Entrez Gene: UIMC1 ubiquitin interaction motif containing 1".
- From UHRF2: "Entrez Gene: UHRF2 ubiquitin-like, containing PHD and RING finger domains, 2".
- From OASL: "Entrez Gene: OASL 2'-5'-oligoadenylate synthetase-like".
- From UBL4A: "Entrez Gene: UBL4A ubiquitin-like 4A".
- From SUMO4: "Entrez Gene: SUMO4 SMT3 suppressor of mif two 3 homolog 4 (S. cerevisiae)".
- From SF3A1: "Entrez Gene: SF3A1 splicing factor 3a, subunit 1, 120kDa".
- From SMN1: "Entrez Gene: SMN1 survival of motor neuron 1, telomeric".
- From UFM1: "Entrez Gene: UFM1 ubiquitin-fold modifier 1".
- From HSPA1L: "Entrez Gene: HSPA1L heat shock 70kDa protein 1-like".
- From HSPA9: "Entrez Gene: HSPA9 heat shock 70kDa protein 9 (mortalin)".
- From UBE1: "Entrez Gene: ubiquitin-like modifier activating enzyme 1".
- From HSPA2: "Entrez Gene: HSPA2 heat shock 70kDa protein 2".
- From Ubiquitin C: "Entrez Gene: UBC ubiquitin C".
- From HLA-B associated transcript 3: "Entrez Gene: BAT3 HLA-B associated transcript 3".
- From RAD23A: "Entrez Gene: RAD23A RAD23 homolog A (S. cerevisiae)".
- From DNAJC10: "Entrez Gene: DNAJC10 DnaJ (Hsp40) homolog, subfamily C, member 10".
- From CYLD (gene): "Entrez Gene: CYLD cylindromatosis (turban tumor syndrome)".
- From ATG7: "Entrez Gene: ATG7 ATG7 autophagy related 7 homolog (S. cerevisiae)".
- From UBE1C: "Entrez Gene: UBE1C ubiquitin-activating enzyme E1C (UBA3 homolog, yeast)".
- From UBE2N: "Entrez Gene: UBE2N ubiquitin-conjugating enzyme E2N (UBC13 homolog, yeast)".
- From RAD23B: "Entrez Gene: RAD23B RAD23 homolog B (S. cerevisiae)".
- From TRAP1: "Entrez Gene: TRAP1 TNF receptor-associated protein 1".
- From CDC34: "Entrez Gene: CDC34 cell division cycle 34 homolog (S. cerevisiae)".
- From DNAJC3: "Entrez Gene: DNAJC3 DnaJ (Hsp40) homolog, subfamily C, member 3".
- From UBE1L2: "Entrez Gene: UBE1L2 ubiquitin-activating enzyme E1-like 2".
- From DNAJB11: "Entrez Gene: DNAJB11 DnaJ (Hsp40) homolog, subfamily B, member 11".
- From UBE2D2: "Entrez Gene: UBE2D2 ubiquitin-conjugating enzyme E2D 2 (UBC4/5 homolog, yeast)".
- From DNAJC6: "Entrez Gene: DNAJC6 DnaJ (Hsp40) homolog, subfamily C, member 6".
- From UBE2G2: "Entrez Gene: UBE2G2 ubiquitin-conjugating enzyme E2G 2 (UBC7 homolog, yeast)".
- From USP6: "Entrez Gene: USP6 ubiquitin specific peptidase 6 (Tre-2 oncogene)".
- From BIRC6: "Entrez Gene: BIRC6 baculoviral IAP repeat-containing 6 (apollon)".
- From HSPA8: "Entrez Gene: HSPA8 heat shock 70kDa protein 8".
- From DNAJC19: "Entrez Gene: DNAJC19 DnaJ (Hsp40) homolog, subfamily C, member 19".
- From APPBP1: "Entrez Gene: APPBP1 amyloid beta precursor protein binding protein 1".
- From DNAJC5: "Entrez Gene: DNAJC5 DnaJ (Hsp40) homolog, subfamily C, member 5".
- From SMN2: "Entrez Gene: survival of motor neuron 2, centromeric".
- From UBE2J1: "Entrez Gene: UBE2J1 ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)".
- From UBE2H: "Entrez Gene: UBE2H ubiquitin-conjugating enzyme E2H (UBC8 homolog, yeast)".
- From UBE1L: "Entrez Gene: UBE1L ubiquitin-activating enzyme E1-like".
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
[edit]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
[edit]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
[edit]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
[edit]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
[edit]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)
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