CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-012373
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Protein RRP5 homolog 
Protein Synonyms/Alias
 NF-kappa-B-binding protein; NFBP; Programmed cell death protein 11 
Gene Name
 PDCD11 
Gene Synonyms/Alias
 KIAA0185 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
58PAKTKKLKIEKRESSubiquitination[1]
173VKLSLNPKNVNRVLSubiquitination[1]
219RAFLPLLKAQEYIRQubiquitination[1, 2, 3]
619LSSDPEPKKEPAGHSubiquitination[4]
790VTNVDEEKQRMLLSLacetylation[5]
1363VSQHSPSKKALYNKHacetylation[5]
1781LGDAERAKAIFENTLubiquitination[2, 3]
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] 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]
 [3] 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]
 [4] 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]
 [5] 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
Functional Description
 Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. Directly interacts with U3 snoRNA. 
Sequence Annotation
 DOMAIN 83 171 S1 motif 1.
 DOMAIN 187 258 S1 motif 2.
 DOMAIN 281 346 S1 motif 3.
 DOMAIN 365 436 S1 motif 4.
 DOMAIN 453 522 S1 motif 5.
 DOMAIN 542 611 S1 motif 6.
 DOMAIN 636 707 S1 motif 7.
 DOMAIN 729 798 S1 motif 8.
 DOMAIN 1036 1109 S1 motif 9.
 DOMAIN 1149 1222 S1 motif 10.
 DOMAIN 1230 1298 S1 motif 11.
 DOMAIN 1324 1396 S1 motif 12.
 REPEAT 1599 1631 HAT 1.
 REPEAT 1705 1737 HAT 2.
 REPEAT 1775 1807 HAT 3.
 REPEAT 1809 1844 HAT 4.
 MOD_RES 2 2 N-acetylalanine.
 MOD_RES 1360 1360 Phosphoserine.
 MOD_RES 1362 1362 Phosphoserine.
 MOD_RES 1493 1493 Phosphoserine.
 MOD_RES 1498 1498 Phosphoserine.  
Keyword
 3D-structure; Acetylation; Complete proteome; Direct protein sequencing; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; rRNA processing. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1871 AA 
Protein Sequence
MANLEESFPR GGTRKIHKPE KAFQQSVEQD NLFDISTEEG STKRKKSQKG PAKTKKLKIE 60
KRESSKSARE KFEILSVESL CEGMRILGCV KEVNELELVI SLPNGLQGFV QVTEICDAYT 120
KKLNEQVTQE QPLKDLLHLP ELFSPGMLVR CVVSSLGITD RGKKSVKLSL NPKNVNRVLS 180
AEALKPGMLL TGTVSSLEDH GYLVDIGVDG TRAFLPLLKA QEYIRQKNKG AKLKVGQYLN 240
CIVEKVKGNG GVVSLSVGHS EVSTAIATEQ QSWNLNNLLP GLVVKAQVQK VTPFGLTLNF 300
LTFFTGVVDF MHLDPKKAGT YFSNQAVRAC ILCVHPRTRV VHLSLRPIFL QPGRPLTRLS 360
CQNLGAVLDD VPVQGFFKKA GATFRLKDGV LAYARLSHLS DSKNVFNPEA FKPGNTHKCR 420
IIDYSQMDEL ALLSLRTSII EAQYLRYHDI EPGAVVKGTV LTIKSYGMLV KVGEQMRGLV 480
PPMHLADILM KNPEKKYHIG DEVKCRVLLC DPEAKKLMMT LKKTLIESKL PVITCYADAK 540
PGLQTHGFII RVKDYGCIVK FYNNVQGLVP KHELSTEYIP DPERVFYTGQ VVKVVVLNCE 600
PSKERMLLSF KLSSDPEPKK EPAGHSQKKG KAINIGQLVD VKVLEKTKDG LEVAVLPHNI 660
RAFLPTSHLS DHVANGPLLH HWLQAGDILH RVLCLSQSEG RVLLCRKPAL VSTVEGGQDP 720
KNFSEIHPGM LLIGFVKSIK DYGVFIQFPS GLSGLAPKAI MSDKFVTSTS DHFVEGQTVA 780
AKVTNVDEEK QRMLLSLRLS DCGLGDLAIT SLLLLNQCLE ELQGVRSLMS NRDSVLIQTL 840
AEMTPGMFLD LVVQEVLEDG SVVFSGGPVP DLVLKASRYH RAGQEVESGQ KKKVVILNVD 900
LLKLEVHVSL HQDLVNRKAR KLRKGSEHQA IVQHLEKSFA IASLVETGHL AAFSLTSHLN 960
DTFRFDSEKL QVGQGVSLTL KTTEPGVTGL LLAVEGPAAK RTMRPTQKDS ETVDEDEEVD 1020
PALTVGTIKK HTLSIGDMVT GTVKSIKPTH VVVTLEDGII GCIHASHILD DVPEGTSPTT 1080
KLKVGKTVTA RVIGGRDMKT FKYLPISHPR FVRTIPELSV RPSELEDGHT ALNTHSVSPM 1140
EKIKQYQAGQ TVTCFLKKYN VVKKWLEVEI APDIRGRIPL LLTSLSFKVL KHPDKKFRVG 1200
QALRATVVGP DSSKTLLCLS LTGPHKLEEG EVAMGRVVKV TPNEGLTVSF PFGKIGTVSI 1260
FHMSDSYSET PLEDFVPQKV VRCYILSTAD NVLTLSLRSS RTNPETKSKV EDPEINSIQD 1320
IKEGQLLRGY VGSIQPHGVF FRLGPSVVGL ARYSHVSQHS PSKKALYNKH LPEGKLLTAR 1380
VLRLNHQKNL VELSFLPGDT GKPDVLSASL EGQLTKQEER KTEAEERDQK GEKKNQKRNE 1440
KKNQKGQEEV EMPSKEKQQP QKPQAQKRGG RECRESGSEQ ERVSKKPKKA GLSEEDDSLV 1500
DVYYREGKEE AEETNVLPKE KQTKPAEAPR LQLSSGFAWN VGLDSLTPAL PPLAESSDSE 1560
EDEKPHQATI KKSKKERELE KQKAEKELSR IEEALMDPGR QPESADDFDR LVLSSPNSSI 1620
LWLQYMAFHL QATEIEKARA VAERALKTIS FREEQEKLNV WVALLNLENM YGSQESLTKV 1680
FERAVQYNEP LKVFLHLADI YAKSEKFQEA GELYNRMLKR FRQEKAVWIK YGAFLLRRSQ 1740
AAASHRVLQR ALECLPSKEH VDVIAKFAQL EFQLGDAERA KAIFENTLST YPKRTDVWSV 1800
YIDMTIKHGS QKDVRDIFER VIHLSLAPKR MKFFFKRYLD YEKQHGTEKD VQAVKAKALE 1860
YVEAKSSVLE D 1871 
Gene Ontology
 GO:0005829; C:cytosol; IEA:Compara.
 GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
 GO:0005634; C:nucleus; IDA:UniProtKB.
 GO:0003723; F:RNA binding; IEA:InterPro.
 GO:0006397; P:mRNA processing; IEA:InterPro.
 GO:0006364; P:rRNA processing; IEA:UniProtKB-KW. 
Interpro
 IPR003107; HAT.
 IPR012340; NA-bd_OB-fold.
 IPR003029; Rbsml_prot_S1_RNA-bd_dom.
 IPR022967; RNA-binding_domain_S1.
 IPR008847; Suf.
 IPR013026; TPR-contain_dom.
 IPR011990; TPR-like_helical. 
Pfam
 PF00575; S1
 PF05843; Suf 
SMART
 SM00386; HAT
 SM00316; S1 
PROSITE
 PS50126; S1 
PRINTS