CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-015259
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 RNA polymerase-associated protein CTR9 homolog 
Protein Synonyms/Alias
 SH2 domain-binding protein 1 
Gene Name
 CTR9 
Gene Synonyms/Alias
 KIAA0155; SH2BP1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
62GKTEEFVKLLEAARIubiquitination[1, 2, 3]
177ACISFNKKDYRGALAubiquitination[4]
188GALAYYKKALRTNPGubiquitination[4]
210GMGHCFVKLNKLEKAubiquitination[4]
252NKEADSIKNGVQLLSubiquitination[2, 4, 5]
357MYIYRGDKENASQCFubiquitination[4]
366NASQCFEKVLKAYPNubiquitination[4]
369QCFEKVLKAYPNNYEubiquitination[2, 4, 5]
379PNNYETMKILGSLYAubiquitination[2, 4]
393AASEDQEKRDIAKGHubiquitination[2, 4, 5]
444ATRILQEKVQADVPPubiquitination[4]
472GNLGEAKKYFLASLDubiquitination[1, 3, 4, 5]
521HEAEKLYKNILREHPubiquitination[4]
544LGAMARDKGNFYEASubiquitination[2, 4]
578IGNLHLAKQEWGPGQubiquitination[4]
637DRALAIYKQVLRNDAubiquitination[4]
645QVLRNDAKNLYAANGubiquitination[1, 3, 4, 5]
660IGAVLAHKGYFREARubiquitination[1, 3, 4, 5]
770RLATSVLKDEKSNLKubiquitination[2]
784KEVLNAVKELELAHRubiquitination[1, 3]
798RYFSYLSKVGDKMRFubiquitination[1, 2, 3]
844EERELRAKQEQEKELubiquitination[2]
849RAKQEQEKELLRQKLubiquitination[2, 4]
884QRAQYVEKTKNILMFacetylation[5]
Reference
 [1] 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]
 [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] 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] 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] 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
 Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non- phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Required for mono- and trimethylation on histone H3 'Lys-4' (H3K4me3) and dimethylation on histone H3 'Lys-79' (H3K4me3). Required for Hox gene transcription. Required for the trimethylation of histone H3 'Lys- 4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of the SET1 complex. Involved in transcriptional regulation of IL6-responsive genes and in JAK-STAT pathway; may regulate DNA- association of STAT3 (By similarity). 
Sequence Annotation
 REPEAT 41 75 TPR 1.
 REPEAT 129 162 TPR 2.
 REPEAT 163 196 TPR 3.
 REPEAT 198 231 TPR 4.
 REPEAT 235 268 TPR 5.
 REPEAT 306 339 TPR 6.
 REPEAT 341 374 TPR 7.
 REPEAT 412 444 TPR 8.
 REPEAT 451 484 TPR 9.
 REPEAT 497 530 TPR 10.
 REPEAT 531 564 TPR 11.
 REPEAT 566 598 TPR 12.
 REPEAT 613 646 TPR 13.
 REPEAT 647 680 TPR 14.
 REPEAT 681 714 TPR 15.
 REPEAT 717 750 TPR 16.
 MOD_RES 925 925 Phosphothreonine.
 MOD_RES 932 932 Phosphoserine.
 MOD_RES 941 941 Phosphoserine.
 MOD_RES 943 943 Phosphoserine.
 MOD_RES 970 970 Phosphoserine.
 MOD_RES 1020 1020 Phosphoserine.
 MOD_RES 1021 1021 Phosphoserine.
 MOD_RES 1039 1039 Phosphoserine (By similarity).
 MOD_RES 1041 1041 Phosphoserine (By similarity).
 MOD_RES 1043 1043 Phosphoserine (By similarity).
 MOD_RES 1081 1081 Phosphoserine (By similarity).
 MOD_RES 1085 1085 Phosphoserine (By similarity).
 MOD_RES 1087 1087 Phosphoserine (By similarity).
 MOD_RES 1097 1097 Phosphoserine.
 MOD_RES 1102 1102 Phosphoserine.  
Keyword
 Complete proteome; Nucleus; Phosphoprotein; Reference proteome; Repeat; TPR repeat; Transcription; Transcription regulation; Wnt signaling pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1173 AA 
Protein Sequence
MSRGSIEIPL RDTDEVIELD FDQLPEGDEV ISILKQEHTQ LHIWIALALE YYKQGKTEEF 60
VKLLEAARID GNLDYRDHEK DQMTCLDTLA AYYVQQARKE KNKDNKKDLI TQATLLYTMA 120
DKIIMYDQNH LLGRACFCLL EGDKMDQADA QFHFVLNQSP NNIPALLGKA CISFNKKDYR 180
GALAYYKKAL RTNPGCPAEV RLGMGHCFVK LNKLEKARLA FSRALELNSK CVGALVGLAV 240
LELNNKEADS IKNGVQLLSR AYTIDPSNPM VLNHLANHFF FKKDYSKVQH LALHAFHNTE 300
VEAMQAESCY QLARSFHVQE DYDQAFQYYY QATQFASSSF VLPFFGLGQM YIYRGDKENA 360
SQCFEKVLKA YPNNYETMKI LGSLYAASED QEKRDIAKGH LKKVTEQYPD DVEAWIELAQ 420
ILEQTDIQGA LSAYGTATRI LQEKVQADVP PEILNNVGAL HFRLGNLGEA KKYFLASLDR 480
AKAEAEHDEH YYNAISVTTS YNLARLYEAM CEFHEAEKLY KNILREHPNY VDCYLRLGAM 540
ARDKGNFYEA SDWFKEALQI NQDHPDAWSL IGNLHLAKQE WGPGQKKFER ILKQPSTQSD 600
TYSMLALGNV WLQTLHQPTR DREKEKRHQD RALAIYKQVL RNDAKNLYAA NGIGAVLAHK 660
GYFREARDVF AQVREATADI SDVWLNLAHI YVEQKQYISA VQMYENCLRK FYKHQNTEVV 720
LYLARALFKC GKLQECKQTL LKARHVAPSD TVLMFNVALV LQRLATSVLK DEKSNLKEVL 780
NAVKELELAH RYFSYLSKVG DKMRFDLALA ATEARQCSDL LSQAQYHVAR ARKQDEEERE 840
LRAKQEQEKE LLRQKLLKEQ EEKRLREKEE QKKLLEQRAQ YVEKTKNILM FTGETEATKE 900
KKRGGGGGRR SKKGGEFDEF VNDDTDDDLP ISKKKKRRKG SGSEQEGEDE EGGERKKKKR 960
RRHPKGEEGS DDDETENGPK PKKRRPPKAE KKKAPKPERL PPSMKGKIKS KAIISSSDDS 1020
SDEDKLKIAD EGHPRNSNSN SDSDEDEQRK KCASSESDSD ENQNKSGSEA GSPRRPRRQR 1080
SDQDSDSDQP SRKRRPSGSE QSDNESVQSG RSHSGVSEND SRPASPSAES DHESERGSDN 1140
EGSGQGSGNE SEPEGSNNEA SDRGSEHGSD DSD 1173 
Gene Ontology
 GO:0016593; C:Cdc73/Paf1 complex; IDA:UniProtKB.
 GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
 GO:0035327; C:transcriptionally active chromatin; ISS:UniProtKB.
 GO:0071222; P:cellular response to lipopolysaccharide; ISS:UniProtKB.
 GO:0001711; P:endodermal cell fate commitment; ISS:UniProtKB.
 GO:0033523; P:histone H2B ubiquitination; IDA:UniProtKB.
 GO:0080182; P:histone H3-K4 trimethylation; IMP:UniProtKB.
 GO:0010390; P:histone monoubiquitination; IDA:UniProtKB.
 GO:0070102; P:interleukin-6-mediated signaling pathway; ISS:UniProtKB.
 GO:0007259; P:JAK-STAT cascade; ISS:UniProtKB.
 GO:0045638; P:negative regulation of myeloid cell differentiation; IDA:UniProtKB.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; ISS:UniProtKB.
 GO:0051571; P:positive regulation of histone H3-K4 methylation; IMP:UniProtKB.
 GO:2001162; P:positive regulation of histone H3-K79 methylation; IMP:UniProtKB.
 GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IDA:UniProtKB.
 GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IDA:UniProtKB.
 GO:0019827; P:stem cell maintenance; IDA:UniProtKB.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0016055; P:Wnt receptor signaling pathway; IEA:UniProtKB-KW. 
Interpro
 IPR001440; TPR-1.
 IPR013026; TPR-contain_dom.
 IPR011990; TPR-like_helical.
 IPR013105; TPR_2.
 IPR019734; TPR_repeat. 
Pfam
 PF00515; TPR_1
 PF07719; TPR_2 
SMART
 SM00028; TPR 
PROSITE
 PS50005; TPR
 PS50293; TPR_REGION 
PRINTS