dbPTM

RL40_HUMAN - PTM Information in dbPTM

Basic Information of Protein

Overview of Protein Modification Sites with Functional and Structural Information
UniProt ID	RL40_HUMAN
UniProt AC	P62987
Protein Name	Ubiquitin-60S ribosomal protein L40
Gene Name	UBA52
Organism	Homo sapiens (Human).
Sequence Length	128
Subcellular Localization	Ubiquitin: Cytoplasm. Nucleus. 60S ribosomal protein L40: Cytoplasm.
Protein Description	Ubiquitin: Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.; 60S ribosomal protein L40: Component of the 60S subunit of the ribosome. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, and especially for cap-dependent translation of vesicular stomatitis virus mRNAs..
Protein Sequence	MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGIIEPSLRQLAQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKKVK

Experimental Post-Translational Modification Sites

* ASA = Accessible Surface Area

Locations	Modification	Substrate Peptides & Secondary Structure	ASA (%)	Reference
6	Acetylation	--MQIFVKTLTGKTI --CEEEEEECCCCEE	27.37	22631001
6	Sumoylation	--MQIFVKTLTGKTI --CEEEEEECCCCEE	27.37	-
6	Methylation	--MQIFVKTLTGKTI --CEEEEEECCCCEE	27.37	22631001
6	Ubiquitination	--MQIFVKTLTGKTI --CEEEEEECCCCEE	27.37	21906983
6	Sumoylation	--MQIFVKTLTGKTI --CEEEEEECCCCEE	27.37	-
7	Phosphorylation	-MQIFVKTLTGKTIT -CEEEEEECCCCEEE	25.01	24043423
9	Phosphorylation	QIFVKTLTGKTITLE EEEEEECCCCEEEEE	41.69	23401153
11	Acetylation	FVKTLTGKTITLEVE EEEECCCCEEEEEEC	31.36	66723255
11	Sumoylation	FVKTLTGKTITLEVE EEEECCCCEEEEEEC	31.36	-
11	Ubiquitination	FVKTLTGKTITLEVE EEEECCCCEEEEEEC	31.36	21906983
11	Sumoylation	FVKTLTGKTITLEVE EEEECCCCEEEEEEC	31.36	-
12	Phosphorylation	VKTLTGKTITLEVEP EEECCCCEEEEEECC	22.12	25159151
14	Phosphorylation	TLTGKTITLEVEPSD ECCCCEEEEEECCCC	23.30	25159151
20	Phosphorylation	ITLEVEPSDTIENVK EEEEECCCCHHHHHH	33.60	21712546
22	Phosphorylation	LEVEPSDTIENVKAK EEECCCCHHHHHHHH	34.23	25159151
27	Sumoylation	SDTIENVKAKIQDKE CCHHHHHHHHHCCCC	56.39	-
27	Ubiquitination	SDTIENVKAKIQDKE CCHHHHHHHHHCCCC	56.39	21906983
27	Sumoylation	SDTIENVKAKIQDKE CCHHHHHHHHHCCCC	56.39	-
29	Ubiquitination	TIENVKAKIQDKEGI HHHHHHHHHCCCCCC	34.87	16543144
29	Sumoylation	TIENVKAKIQDKEGI HHHHHHHHHCCCCCC	34.87	-
33	Sumoylation	VKAKIQDKEGIPPDQ HHHHHCCCCCCCHHH	41.27	-
33	Ubiquitination	VKAKIQDKEGIPPDQ HHHHHCCCCCCCHHH	41.27	21906983
48	Sumoylation	QRLIFAGKQLEDGRT HEEEEEEEECCCCCC	48.56	-
48	Ubiquitination	QRLIFAGKQLEDGRT HEEEEEEEECCCCCC	48.56	16443603
48	Sumoylation	QRLIFAGKQLEDGRT HEEEEEEEECCCCCC	48.56	-
48	Acetylation	QRLIFAGKQLEDGRT HEEEEEEEECCCCCC	48.56	14501331
55	Phosphorylation	KQLEDGRTLSDYNIQ EECCCCCCCCCCCCC	35.82	25159151
57	Phosphorylation	LEDGRTLSDYNIQKE CCCCCCCCCCCCCCH	37.12	23401153
59	Nitration	DGRTLSDYNIQKEST CCCCCCCCCCCCHHH	15.70	-
59	Phosphorylation	DGRTLSDYNIQKEST CCCCCCCCCCCCHHH	15.70	23911959
63	Ubiquitination	LSDYNIQKESTLHLV CCCCCCCCHHHHHHH	50.24	21906983
63	Sumoylation	LSDYNIQKESTLHLV CCCCCCCCHHHHHHH	50.24	-
63	Sumoylation	LSDYNIQKESTLHLV CCCCCCCCHHHHHHH	50.24	-
63	Methylation	LSDYNIQKESTLHLV CCCCCCCCHHHHHHH	50.24	66693181
65	Phosphorylation	DYNIQKESTLHLVLR CCCCCCHHHHHHHHH	43.22	28355574
66	Phosphorylation	YNIQKESTLHLVLRL CCCCCHHHHHHHHHH	21.20	22617229
72	Methylation	STLHLVLRLRGGIIE HHHHHHHHHCCCCCC	18.17	-
76	ADP-ribosylation	LVLRLRGGIIEPSLR HHHHHCCCCCCHHHH	15.97	28525742
81	Phosphorylation	RGGIIEPSLRQLAQK CCCCCCHHHHHHHHH	24.32	25954137
88	Ubiquitination	SLRQLAQKYNCDKMI HHHHHHHHCCCCHHH	32.59	21890473
88	Acetylation	SLRQLAQKYNCDKMI HHHHHHHHCCCCHHH	32.59	25825284
91	S-nitrosocysteine	QLAQKYNCDKMICRK HHHHHCCCCHHHHHH	4.89	-
91	S-nitrosylation	QLAQKYNCDKMICRK HHHHHCCCCHHHHHH	4.89	19483679
93	Ubiquitination	AQKYNCDKMICRKCY HHHCCCCHHHHHHHH	32.15	-
93	Acetylation	AQKYNCDKMICRKCY HHHCCCCHHHHHHHH	32.15	25825284
98	"N6,N6,N6-trimethyllysine"	CDKMICRKCYARLHP CCHHHHHHHHHHHCH	27.47	-
98	Methylation	CDKMICRKCYARLHP CCHHHHHHHHHHHCH	27.47	116252499
100	Phosphorylation	KMICRKCYARLHPRA HHHHHHHHHHHCHHH	9.59	29759185
115	S-nitrosylation	VNCRKKKCGHTNNLR HCCCHHCCCCCCCCC	7.11	2212679

Upstream regulatory proteins (kinases for phosphorylation sites, E3 ubiquitin ligases of ubiquitination sites, ...)

Modified Location	Modified Residue	Modification	Type of Upstream Proteins	Gene Name of Upstream Proteins	UniProt AC of Upstream Proteins	Sources
65	S	Phosphorylation	Kinase	PINK1	Q9BXM7	Uniprot

Functions of PTM Sites

Modified Location	Modified Residue	Modification	Reference
65	S	Phosphorylation	24660806
[Ubiquitin]: Phosphorylated at Ser-65 by PINK1 during mitophagy.
65	S	ubiquitylation	24660806
[Ubiquitin]: Phosphorylated at Ser-65 by PINK1 during mitophagy.

Disease-associated PTM Sites based on SAP

* Distance = the distance between SAP position and PTM sites.

Modified Location	Modification	Variant Position (Distance <= 10)	Residue Change	SAP	Related Disease	Reference
Oops, there are no SNP-PTM records of RL40_HUMAN !!

Protein-Protein Interaction

Interacting Protein	Gene Name	Interaction Type	PPI Reference
VDAC2_HUMAN	VDAC2	physical	22939629
USP9X_HUMAN	USP9X	physical	22939629
VDAC3_HUMAN	VDAC3	physical	22939629
VDAC1_HUMAN	VDAC1	physical	22939629
UNK_HUMAN	UNK	physical	22939629
ZRAB2_HUMAN	ZRANB2	physical	22939629
ANCHR_HUMAN	ZFYVE19	physical	22939629
ZSC18_HUMAN	ZSCAN18	physical	22939629
VAMP2_HUMAN	VAMP2	physical	22939629
UFM1_HUMAN	UFM1	physical	22939629
UFC1_HUMAN	UFC1	physical	22939629
RAB2A_HUMAN	RAB2A	physical	26344197
RL13_HUMAN	RPL13	physical	26344197
RL35_HUMAN	RPL35	physical	26344197
RL35A_HUMAN	RPL35A	physical	26344197
RL4_HUMAN	RPL4	physical	26344197
RLA2_HUMAN	RPLP2	physical	26344197
RS4X_HUMAN	RPS4X	physical	26344197

Drug and Disease Associations

Kegg Disease
There are no disease associations of PTM sites.
OMIM Disease
There are no disease associations of PTM sites.
Kegg Drug
There are no disease associations of PTM sites.
DrugBank
There are no disease associations of PTM sites.

Regulatory Network of RL40_HUMAN

Related Literatures of Post-Translational Modification

Acetylation
Reference	PubMed
"Lysine acetylation targets protein complexes and co-regulates majorcellular functions."; Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.,Olsen J.V., Mann M.; Science 325:834-840(2009). Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-6 AND LYS-48, AND MASSSPECTROMETRY.	19608861 [Abstract]
Phosphorylation
Reference	PubMed
"Global, in vivo, and site-specific phosphorylation dynamics insignaling networks."; Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P.,Mann M.; Cell 127:635-648(2006). Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-65, AND MASSSPECTROMETRY.	17081983 [Abstract]
Ubiquitylation
Reference	PubMed
"Polyubiquitination of proliferating cell nuclear antigen by HLTF andSHPRH prevents genomic instability from stalled replication forks."; Motegi A., Liaw H.-J., Lee K.-Y., Roest H.P., Maas A., Wu X.,Moinova H., Markowitz S.D., Ding H., Hoeijmakers J.H.J., Myung K.; Proc. Natl. Acad. Sci. U.S.A. 105:12411-12416(2008). Cited for: UBIQUITINATION AT LYS-63, AND MUTAGENESIS OF LYS-48 AND LYS-63.	18719106 [Abstract]
"The proteomic reactor facilitates the analysis of affinity-purifiedproteins by mass spectrometry: application for identifyingubiquitinated proteins in human cells."; Vasilescu J., Zweitzig D.R., Denis N.J., Smith J.C., Ethier M.,Haines D.S., Figeys D.; J. Proteome Res. 6:298-305(2007). Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-48, AND MASSSPECTROMETRY.	17203973 [Abstract]
"Mass spectrometric characterization of the affinity-purified human26S proteasome complex."; Wang X., Chen C.-F., Baker P.R., Chen P.-L., Kaiser P., Huang L.; Biochemistry 46:3553-3565(2007). Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-48, AND MASSSPECTROMETRY.	17323924 [Abstract]
"Differential regulation of EGF receptor internalization anddegradation by multiubiquitination within the kinase domain."; Huang F., Kirkpatrick D., Jiang X., Gygi S.P., Sorkin A.; Mol. Cell 21:737-748(2006). Cited for: FUNCTION, UBIQUITINATION AT LYS-11; LYS-29; LYS-48 AND LYS-63, ANDMASS SPECTROMETRY.	16543144 [Abstract]
"Alzheimer disease-specific conformation of hyperphosphorylated pairedhelical filament-tau is polyubiquitinated through Lys-48, Lys-11, andLys-6 ubiquitin conjugation."; Cripps D., Thomas S.N., Jeng Y., Yang F., Davies P., Yang A.J.; J. Biol. Chem. 281:10825-10838(2006). Cited for: PROTEIN SEQUENCE OF 1-27 AND 43-54, UBIQUITINATION AT LYS-6; LYS-11AND LYS-48, AND MASS SPECTROMETRY.	16443603 [Abstract]

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