CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-000109
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Nucleolar protein 56 
Protein Synonyms/Alias
 Nucleolar protein 5A 
Gene Name
 NOP56 
Gene Synonyms/Alias
 NOL5A 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
87LETHLPSKKKKVLLGubiquitination[1]
88ETHLPSKKKKVLLGVubiquitination[2, 3]
89THLPSKKKKVLLGVGubiquitination[2]
90HLPSKKKKVLLGVGDubiquitination[2, 3]
134LHFHNLVKGLTDLSAubiquitination[2]
143LTDLSACKAQLGLGHubiquitination[2, 3]
227RRELNEDKLEKLEELubiquitination[2, 3, 4]
230LNEDKLEKLEELTMDubiquitination[2, 4]
240ELTMDGAKAKAILDAubiquitination[1, 2]
242TMDGAKAKAILDASRubiquitination[2, 5]
288LHTYLRSKMSQVAPSubiquitination[1, 2, 4]
320GSLTNLAKYPASTVQubiquitination[1, 2, 4, 6, 7]
333VQILGAEKALFRALKubiquitination[1, 2, 4, 5, 6, 7, 8]
375ISRYLANKCSIASRIubiquitination[2, 5]
396PTSVFGEKLREQVEEubiquitination[2, 5]
422RKNLDVMKEAMVQAEubiquitination[1]
478ECEEMSEKPKKKKKQmethylation[9]
478ECEEMSEKPKKKKKQubiquitination[2]
480EEMSEKPKKKKKQKPmethylation[9]
505DPSISFSKPKKKKSFacetylation[10, 11]
Reference
 [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] 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]
 [3] 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]
 [4] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [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] 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]
 [9] Large-scale global identification of protein lysine methylation in vivo.
 Cao XJ, Arnaudo AM, Garcia BA.
 Epigenetics. 2013 May 1;8(5):477-85. [PMID: 23644510]
 [10] 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]
 [11] 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
 Involved in the early to middle stages of 60S ribosomal subunit biogenesis. 
Sequence Annotation
 DOMAIN 292 410 Nop.
 MOD_RES 314 314 Phosphoserine.
 MOD_RES 467 467 Phosphoserine (By similarity).
 MOD_RES 468 468 Phosphothreonine (By similarity).
 MOD_RES 511 511 Phosphoserine.
 MOD_RES 519 519 Phosphoserine.
 MOD_RES 520 520 Phosphoserine.
 MOD_RES 569 569 Phosphoserine.
 MOD_RES 570 570 Phosphoserine.
 MOD_RES 579 579 Phosphoserine.
 MOD_RES 581 581 Phosphoserine.  
Keyword
 Complete proteome; Cytoplasm; Direct protein sequencing; Neurodegeneration; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Ribosome biogenesis; Spinocerebellar ataxia. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 594 AA 
Protein Sequence
MVLLHVLFEH AVGYALLALK EVEEISLLQP QVEESVLNLG KFHSIVRLVA FCPFASSQVA 60
LENANAVSEG VVHEDLRLLL ETHLPSKKKK VLLGVGDPKI GAAIQEELGY NCQTGGVIAE 120
ILRGVRLHFH NLVKGLTDLS ACKAQLGLGH SYSRAKVKFN VNRVDNMIIQ SISLLDQLDK 180
DINTFSMRVR EWYGYHFPEL VKIINDNATY CRLAQFIGNR RELNEDKLEK LEELTMDGAK 240
AKAILDASRS SMGMDISAID LINIESFSSR VVSLSEYRQS LHTYLRSKMS QVAPSLSALI 300
GEAVGARLIA HAGSLTNLAK YPASTVQILG AEKALFRALK TRGNTPKYGL IFHSTFIGRA 360
AAKNKGRISR YLANKCSIAS RIDCFSEVPT SVFGEKLREQ VEERLSFYET GEIPRKNLDV 420
MKEAMVQAEE AAAEITRKLE KQEKKRLKKE KKRLAALALA SSENSSSTPE ECEEMSEKPK 480
KKKKQKPQEV PQENGMEDPS ISFSKPKKKK SFSKEELMSS DLEETAGSTS IPKRKKSTPK 540
EETVNDPEEA GHRSGSKKKR KFSKEEPVSS GPEEAVGKSS SKKKKKFHKA SQED 594 
Gene Ontology
 GO:0031428; C:box C/D snoRNP complex; NAS:BHF-UCL.
 GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
 GO:0070761; C:pre-snoRNP complex; IDA:BHF-UCL.
 GO:0030515; F:snoRNA binding; IDA:BHF-UCL.
 GO:0008219; P:cell death; IEA:UniProtKB-KW.
 GO:0006364; P:rRNA processing; TAS:ProtInc. 
Interpro
 IPR012974; NOP5_N.
 IPR002687; Nop_dom.
 IPR012976; NOSIC. 
Pfam
 PF01798; Nop
 PF08156; NOP5NT
 PF08060; NOSIC 
SMART
 SM00931; NOSIC 
PROSITE
 PS51358; NOP 
PRINTS