CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-008481
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Heterogeneous nuclear ribonucleoprotein M 
Protein Synonyms/Alias
 hnRNP M 
Gene Name
 HNRNPM 
Gene Synonyms/Alias
 HNRPM; NAGR1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
17EVAATEIKMEEESGAsumoylation[1, 2]
37GNGAPGPKGEGERPAubiquitination[3, 4]
48ERPAQNEKRKEKNIKubiquitination[3, 5]
69EPYANPTKRYRAFITubiquitination[3, 4, 5, 6, 7]
83TNIPFDVKWQSLKDLubiquitination[3, 4, 5, 6, 7, 8, 9]
88DVKWQSLKDLVKEKVubiquitination[3, 4, 5, 6, 7, 9]
92QSLKDLVKEKVGEVTubiquitination[4, 5]
94LKDLVKEKVGEVTYVubiquitination[4]
110LLMDAEGKSRGCAVVubiquitination[3, 4, 5]
120GCAVVEFKMEESMKKubiquitination[4]
126FKMEESMKKAAEVLNubiquitination[3]
134KAAEVLNKHSLSGRPubiquitination[3, 4, 5, 9, 10]
145SGRPLKVKEDPDGEHsumoylation[2]
145SGRPLKVKEDPDGEHubiquitination[3, 5]
159HARRAMQKVMATTGGubiquitination[3]
214FVANLDYKVGWKKLKubiquitination[3]
221KVGWKKLKEVFSMAGubiquitination[3]
239RADILEDKDGKSRGIacetylation[11]
239RADILEDKDGKSRGIubiquitination[3, 4, 5]
242ILEDKDGKSRGIGTVubiquitination[3, 4]
277FDRPMHVKMDERALPacetylation[12]
285MDERALPKGDFFPPEubiquitination[4]
345GIGFGINKMGGMEGPubiquitination[3, 5]
381EILSNALKRGEIIAKubiquitination[3, 4, 5, 6, 7, 9, 13]
388KRGEIIAKQGGGGGGubiquitination[3, 4, 5, 6, 7, 13]
651HAPGVARKACQIFVRmethylation[14]
651HAPGVARKACQIFVRubiquitination[3, 4, 5, 6, 7, 9, 10]
667LPFDFTWKMLKDKFNsumoylation[2]
667LPFDFTWKMLKDKFNubiquitination[3, 4, 6, 7, 8, 9]
670DFTWKMLKDKFNECGubiquitination[4, 5]
672TWKMLKDKFNECGHVacetylation[15]
672TWKMLKDKFNECGHVubiquitination[4, 5, 9]
685HVLYADIKMENGKSKacetylation[15]
685HVLYADIKMENGKSKubiquitination[3, 4, 5, 15, 16]
690DIKMENGKSKGCGVVubiquitination[3]
692KMENGKSKGCGVVKFubiquitination[3, 5]
698SKGCGVVKFESPEVAacetylation[12, 15, 17, 18]
698SKGCGVVKFESPEVAsumoylation[1]
698SKGCGVVKFESPEVAubiquitination[3, 4, 5, 6, 7, 9, 15]
716CRMMNGMKLSGREIDubiquitination[3, 4, 5, 6, 7, 15, 16]
Reference
 [1] Site-specific identification of SUMO-2 targets in cells reveals an inverted SUMOylation motif and a hydrophobic cluster SUMOylation motif.
 Matic I, Schimmel J, Hendriks IA, van Santen MA, van de Rijke F, van Dam H, Gnad F, Mann M, Vertegaal AC.
 Mol Cell. 2010 Aug 27;39(4):641-52. [PMID: 20797634]
 [2] Targeted identification of SUMOylation sites in human proteins using affinity enrichment and paralog-specific reporter ions.
 Lamoliatte F, Bonneil E, Durette C, Caron-Lizotte O, Wildemann D, Zerweck J, Wenschuh H, Thibault P.
 Mol Cell Proteomics. 2013 Jun 7;. [PMID: 23750026]
 [3] 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]
 [4] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [10] Proteomic analyses reveal divergent ubiquitylation site patterns in murine tissues.
 Wagner SA, Beli P, Weinert BT, Schölz C, Kelstrup CD, Young C, Nielsen ML, Olsen JV, Brakebusch C, Choudhary C.
 Mol Cell Proteomics. 2012 Dec;11(12):1578-85. [PMID: 22790023]
 [11] Spermidine and resveratrol induce autophagy by distinct pathways converging on the acetylproteome.
 Morselli E, Mariño G, Bennetzen MV, Eisenberg T, Megalou E, Schroeder S, Cabrera S, Bénit P, Rustin P, Criollo A, Kepp O, Galluzzi L, Shen S, Malik SA, Maiuri MC, Horio Y, López-Otín C, Andersen JS, Tavernarakis N, Madeo F, Kroemer G.
 J Cell Biol. 2011 Feb 21;192(4):615-29. [PMID: 21339330]
 [12] 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]
 [13] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [14] Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome.
 Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T.
 Mol Biosyst. 2013 Jul 30;9(9):2231-47. [PMID: 23748837]
 [15] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [16] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [17] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [18] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377
Functional Description
 Pre-mRNA binding protein in vivo, binds avidly to poly(G) and poly(U) RNA homopolymers in vitro. Involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells, may initiate a series of signaling events leading to tyrosine phosphorylation of proteins and induction of IL-1 alpha, IL-6, IL-10 and tumor necrosis factor alpha cytokines. 
Sequence Annotation
 DOMAIN 71 149 RRM 1.
 DOMAIN 204 281 RRM 2.
 REPEAT 400 405 1.
 REPEAT 407 412 2.
 REPEAT 415 420 3.
 REPEAT 426 431 4.
 REPEAT 433 438 5.
 REPEAT 440 445 6.
 REPEAT 446 451 7.
 REPEAT 453 458 8.
 REPEAT 461 466 9.
 REPEAT 468 473 10.
 REPEAT 475 480 11.
 REPEAT 482 487 12.
 REPEAT 493 498 13.
 REPEAT 500 505 14.
 REPEAT 507 512 15.
 REPEAT 514 519 16.
 REPEAT 521 526 17.
 REPEAT 528 533 18.
 REPEAT 540 545 19.
 REPEAT 547 552 20.
 REPEAT 554 559 21.
 REPEAT 562 567 22.
 REPEAT 567 572 23.
 REPEAT 575 580 24.
 REPEAT 580 585 25.
 REPEAT 588 593 26.
 REPEAT 603 608 27.
 DOMAIN 653 729 RRM 3.
 REGION 400 608 27 X 6 AA repeats of [GEVSTPAN]-[ILMV]-
 MOD_RES 2 2 N-acetylalanine.
 MOD_RES 29 29 Phosphoserine.
 MOD_RES 277 277 N6-acetyllysine.
 MOD_RES 432 432 Phosphoserine.
 MOD_RES 452 452 Phosphoserine.
 MOD_RES 468 468 Phosphoserine.
 MOD_RES 481 481 Phosphoserine.
 MOD_RES 528 528 Phosphoserine.
 MOD_RES 575 575 Phosphoserine.
 MOD_RES 588 588 Phosphoserine.
 MOD_RES 618 618 Phosphoserine.
 MOD_RES 633 633 Phosphoserine.
 MOD_RES 637 637 Phosphoserine.
 MOD_RES 698 698 N6-acetyllysine.
 MOD_RES 701 701 Phosphoserine.  
Keyword
 3D-structure; Acetylation; Alternative splicing; Complete proteome; Direct protein sequencing; mRNA processing; mRNA splicing; Nucleus; Phosphoprotein; Reference proteome; Repeat; Ribonucleoprotein; RNA-binding; Spliceosome; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 730 AA 
Protein Sequence
MAAGVEAAAE VAATEIKMEE ESGAPGVPSG NGAPGPKGEG ERPAQNEKRK EKNIKRGGNR 60
FEPYANPTKR YRAFITNIPF DVKWQSLKDL VKEKVGEVTY VELLMDAEGK SRGCAVVEFK 120
MEESMKKAAE VLNKHSLSGR PLKVKEDPDG EHARRAMQKV MATTGGMGMG PGGPGMITIP 180
PSILNNPNIP NEIIHALQAG RLGSTVFVAN LDYKVGWKKL KEVFSMAGVV VRADILEDKD 240
GKSRGIGTVT FEQSIEAVQA ISMFNGQLLF DRPMHVKMDE RALPKGDFFP PERPQQLPHG 300
LGGIGMGLGP GGQPIDANHL NKGIGMGNIG PAGMGMEGIG FGINKMGGME GPFGGGMENM 360
GRFGSGMNMG RINEILSNAL KRGEIIAKQG GGGGGGSVPG IERMGPGIDR LGGAGMERMG 420
AGLGHGMDRV GSEIERMGLV MDRMGSVERM GSGIERMGPL GLDHMASSIE RMGQTMERIG 480
SGVERMGAGM GFGLERMAAP IDRVGQTIER MGSGVERMGP AIERMGLSME RMVPAGMGAG 540
LERMGPVMDR MATGLERMGA NNLERMGLER MGANSLERMG LERMGANSLE RMGPAMGPAL 600
GAGIERMGLA MGGGGGASFD RAIEMERGNF GGSFAGSFGG AGGHAPGVAR KACQIFVRNL 660
PFDFTWKMLK DKFNECGHVL YADIKMENGK SKGCGVVKFE SPEVAERACR MMNGMKLSGR 720
EIDVRIDRNA 730 
Gene Ontology
 GO:0071013; C:catalytic step 2 spliceosome; IDA:UniProtKB.
 GO:0005887; C:integral to plasma membrane; TAS:ProtInc.
 GO:0016363; C:nuclear matrix; IDA:BHF-UCL.
 GO:0042382; C:paraspeckles; IDA:BHF-UCL.
 GO:0000166; F:nucleotide binding; IEA:InterPro.
 GO:0003723; F:RNA binding; NAS:HGNC.
 GO:0000380; P:alternative mRNA splicing, via spliceosome; IMP:BHF-UCL. 
Interpro
 IPR024667; HnRNP_M.
 IPR024666; HnRNP_M_PY-NLS.
 IPR012677; Nucleotide-bd_a/b_plait.
 IPR000504; RRM_dom. 
Pfam
 PF11532; HnRNP_M
 PF00076; RRM_1 
SMART
 SM00360; RRM 
PROSITE
 PS50102; RRM 
PRINTS