CPLM-012237

Genbank Nucleotide ID

Heterogeneous nuclear ribonucleoprotein D0

Protein Synonyms/Alias

hnRNP D0; AU-rich element RNA-binding protein 1

Homo sapiens (Human)

Position	Peptide	Type	References
72	GAKIDASKNEEDEGH	ubiquitination	[1]
110	GLSWDTTKKDLKDYF	ubiquitination	[1, 2]
114	DTTKKDLKDYFSKFG	ubiquitination	[3, 4, 5]
119	DLKDYFSKFGEVVDC	methylation	[6]
119	DLKDYFSKFGEVVDC	ubiquitination	[3, 4, 5]
129	EVVDCTLKLDPITGR	ubiquitination	[1, 2, 7]
165	KEHKLNGKVIDPKRA	acetylation	[8]
170	NGKVIDPKRAKAMKT	ubiquitination	[9]
183	KTKEPVKKIFVGGLS	ubiquitination	[3, 4, 5]
197	SPDTPEEKIREYFGG	ubiquitination	[1, 2, 3, 4, 5, 7, 10, 11]
218	IELPMDNKTNKRRGF	ubiquitination	[1]
251	YHNVGLSKCEIKVAM	acetylation	[8]
251	YHNVGLSKCEIKVAM	ubiquitination	[4]
260	EIKVAMSKEQYQQQQ	ubiquitination	[1]
353	GGHQNSYKPY*****	acetylation	[8]

[1] Systematic and quantitative assessment of the ubiquitin-modified proteome.
Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
[2] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
[3] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
[4] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
[5] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
Chen Z, Zhou Y, Song J, Zhang Z.
Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
[6] Update on activities at the Universal Protein Resource (UniProt) in 2013.
e="String">UniProt Consortium.
Nucleic Acids Res. 2013 Jan;41(Database issue):D43-7. [PMID: 23161681]
[7] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931]
[8] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861]
[9] Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry.
Denis NJ, Vasilescu J, Lambert JP, Smith JC, Figeys D.
Proteomics. 2007 Mar;7(6):868-74. [PMID: 17370265]
[10] Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling.
Xu G, Paige JS, Jaffrey SR.
Nat Biotechnol. 2010 Aug;28(8):868-73. [PMID: 20639865]
[11] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048]

Functional Description

Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto- oncogenes and cytokine mRNAs. Also binds to double- and single- stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'- TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain.

DOMAIN 97 179 RRM 1.
DOMAIN 182 261 RRM 2.
MOD_RES 71 71 Phosphoserine.
MOD_RES 80 80 Phosphoserine.
MOD_RES 82 82 Phosphoserine.
MOD_RES 83 83 Phosphoserine.
MOD_RES 119 119 N6-methyllysine.
MOD_RES 165 165 N6-acetyllysine.
MOD_RES 190 190 Phosphoserine.
MOD_RES 193 193 Phosphothreonine.
MOD_RES 251 251 N6-acetyllysine.
MOD_RES 345 345 Dimethylated arginine.

3D-structure; Acetylation; Alternative splicing; Complete proteome; Cytoplasm; Direct protein sequencing; DNA-binding; Methylation; Nucleus; Phosphoprotein; Reference proteome; Repeat; Ribonucleoprotein; RNA-binding; Transcription; Transcription regulation.

UniProt (SWISSPROT/TrEMBL); GenBank; EMBL

GO:0005829; C:cytosol; TAS:Reactome.
GO:0005654; C:nucleoplasm; TAS:Reactome.
GO:0030529; C:ribonucleoprotein complex; IDA:UniProtKB.
GO:0000166; F:nucleotide binding; IEA:InterPro.
GO:0003723; F:RNA binding; IDA:UniProtKB.
GO:0042162; F:telomeric DNA binding; IDA:UniProtKB.
GO:0000398; P:mRNA splicing, via spliceosome; TAS:Reactome.
GO:0045893; P:positive regulation of transcription, DNA-dependent; NAS:UniProtKB.
GO:0043488; P:regulation of mRNA stability; IEA:Compara.
GO:0006401; P:RNA catabolic process; TAS:ProtInc.
GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW.

IPR012956; CARG-binding_factor_N.
IPR012677; Nucleotide-bd_a/b_plait.
IPR000504; RRM_dom.

PF08143; CBFNT
PF00076; RRM_1