CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-001009
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 H/ACA ribonucleoprotein complex subunit 4 
Protein Synonyms/Alias
 CBF5 homolog; Dyskerin; Nopp140-associated protein of 57 kDa; Nucleolar protein NAP57; Nucleolar protein family A member 4; snoRNP protein DKC1 
Gene Name
 DKC1 
Gene Synonyms/Alias
 NOLA4 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
12EVIILPKKHKKKKERubiquitination[1]
20HKKKKERKSLPEEDVubiquitination[1, 2]
39HAEEFLIKPESKVAKubiquitination[1, 2, 3]
43FLIKPESKVAKLDTSubiquitination[2]
46KPESKVAKLDTSQWPubiquitination[1, 2, 3]
57SQWPLLLKNFDKLNVubiquitination[1, 2, 3]
61LLLKNFDKLNVRTTHubiquitination[1]
80ACGSNPLKREIGDYIubiquitination[1, 4]
96TGFINLDKPSNPSSHubiquitination[1]
117RRILRVEKTGHSGTLubiquitination[1]
151KSQQSAGKEYVGIVRubiquitination[1, 2]
191PPLIAAVKRQLRVRTubiquitination[1, 3, 5]
203VRTIYESKMIEYDPEubiquitination[1, 2]
257RSGVMSEKDHMVTMHubiquitination[1]
302SHKRLVMKDSAVNAIubiquitination[1]
379ERDTYPRKWGLGPKAubiquitination[1]
385RKWGLGPKASQKKLMubiquitination[1]
394SQKKLMIKQGLLDKHubiquitination[1, 5, 6]
403GLLDKHGKPTDSTPAubiquitination[1, 2]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [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] 
Functional Description
 Isoform 1: Required for ribosome biogenesis and telomere maintenance. Probable catalytic subunit of H/ACA small nucleolar ribonucleoprotein (H/ACA snoRNP) complex, which catalyzes pseudouridylation of rRNA. This involves the isomerization of uridine such that the ribose is subsequently attached to C5, instead of the normal N1. Each rRNA can contain up to 100 pseudouridine ('psi') residues, which may serve to stabilize the conformation of rRNAs. Also required for correct processing or intranuclear trafficking of TERC, the RNA component of the telomerase reverse transcriptase (TERT) holoenzyme. 
Sequence Annotation
 DOMAIN 296 371 PUA.
 REGION 2 21 Nucleolar localization.
 REGION 446 514 Nuclear and nucleolar localization.
 ACT_SITE 125 125 Nucleophile (By similarity).
 MOD_RES 2 2 N-acetylalanine.
 MOD_RES 21 21 Phosphoserine.
 MOD_RES 451 451 Phosphoserine.
 MOD_RES 453 453 Phosphoserine.
 MOD_RES 455 455 Phosphoserine.
 MOD_RES 458 458 Phosphothreonine (By similarity).
 MOD_RES 485 485 Phosphoserine.
 MOD_RES 494 494 Phosphoserine.
 MOD_RES 513 513 Phosphoserine.  
Keyword
 Acetylation; Alternative splicing; Complete proteome; Cytoplasm; Direct protein sequencing; Disease mutation; Dyskeratosis congenita; Isomerase; Nucleus; Phosphoprotein; Reference proteome; Ribonucleoprotein; Ribosome biogenesis; RNA-binding; rRNA processing. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 514 AA 
Protein Sequence
MADAEVIILP KKHKKKKERK SLPEEDVAEI QHAEEFLIKP ESKVAKLDTS QWPLLLKNFD 60
KLNVRTTHYT PLACGSNPLK REIGDYIRTG FINLDKPSNP SSHEVVAWIR RILRVEKTGH 120
SGTLDPKVTG CLIVCIERAT RLVKSQQSAG KEYVGIVRLH NAIEGGTQLS RALETLTGAL 180
FQRPPLIAAV KRQLRVRTIY ESKMIEYDPE RRLGIFWVSC EAGTYIRTLC VHLGLLLGVG 240
GQMQELRRVR SGVMSEKDHM VTMHDVLDAQ WLYDNHKDES YLRRVVYPLE KLLTSHKRLV 300
MKDSAVNAIC YGAKIMLPGV LRYEDGIEVN QEIVVITTKG EAICMAIALM TTAVISTCDH 360
GIVAKIKRVI MERDTYPRKW GLGPKASQKK LMIKQGLLDK HGKPTDSTPA TWKQEYVDYS 420
ESAKKEVVAE VVKAPQVVAE AAKTAKRKRE SESESDETPP AAPQLIKKEK KKSKKDKKAK 480
AGLESGAEPG DGDSDTTKKK KKKKKAKEVE LVSE 514 
Gene Ontology
 GO:0015030; C:Cajal body; IEA:UniProtKB-SubCell.
 GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
 GO:0005730; C:nucleolus; IDA:HPA.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0005697; C:telomerase holoenzyme complex; IDA:UniProtKB.
 GO:0009982; F:pseudouridine synthase activity; IEA:InterPro.
 GO:0003723; F:RNA binding; TAS:ProtInc.
 GO:0003720; F:telomerase activity; IDA:UniProtKB.
 GO:0008283; P:cell proliferation; TAS:ProtInc.
 GO:0001522; P:pseudouridine synthesis; IEA:InterPro.
 GO:0006364; P:rRNA processing; TAS:ProtInc.
 GO:0007004; P:telomere maintenance via telomerase; TAS:Reactome. 
Interpro
 IPR012960; Dyskerin-like.
 IPR002501; PsdUridine_synth.
 IPR020103; PsdUridine_synth_cat_dom.
 IPR002478; PUA.
 IPR015947; PUA-like_domain.
 IPR004802; tRNA_PsdUridine_synth_B_fam.
 IPR004521; Uncharacterised_CHP00451. 
Pfam
 PF08068; DKCLD
 PF01472; PUA
 PF01509; TruB_N 
SMART
 SM00359; PUA 
PROSITE
 PS50890; PUA 
PRINTS