CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-021681
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Pre-mRNA-splicing factor SYF1 
Protein Synonyms/Alias
 Protein HCNP; XPA-binding protein 2 
Gene Name
 XAB2 
Gene Synonyms/Alias
 HCNP; KIAA1177; SYF1; PP3898 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
36MRNQFSVKCWLRYIEubiquitination[1]
45WLRYIEFKQGAPKPRubiquitination[1]
62QLYERALKLLPCSYKubiquitination[1]
69KLLPCSYKLWYRYLKubiquitination[1]
174RGYRRFLKLSPESAEubiquitination[1, 2, 3]
188EEYIEYLKSSDRLDEubiquitination[1, 2, 3]
389VQTVDPFKATGKPHTubiquitination[1]
393DPFKATGKPHTLWVAubiquitination[1]
420DARVILEKATKVNFKacetylation[4]
420DARVILEKATKVNFKubiquitination[1, 2]
423VILEKATKVNFKQVDubiquitination[1]
458EALRLLRKATALPARubiquitination[1]
539KYFEESFKAYERGISubiquitination[2]
593GCPPKYAKTLYLLYAubiquitination[1]
637DMFNIYIKRAAEIYGubiquitination[1, 2, 3]
654HTRGIYQKAIEVLSDubiquitination[1, 2, 3, 5]
677RFADMECKLGEIDRAubiquitination[1, 2]
708GAFWQTWKDFEVRHGubiquitination[1, 2, 3, 5, 6, 7]
721HGNEDTIKEMLRIRRubiquitination[1, 2, 3]
770QSGMDDMKLLEQRAEubiquitination[1, 2, 3]
794QPLRAQSKILFVRSDubiquitination[1, 8]
853AAVFGSLKED*****ubiquitination[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] 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]
 [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] 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] 
Functional Description
 Involved in transcription-coupled repair (TCR), transcription and pre-mRNA splicing. 
Sequence Annotation
 REPEAT 15 47 HAT 1.
 REPEAT 48 80 HAT 2.
 REPEAT 90 122 HAT 3.
 REPEAT 124 158 HAT 4.
 REPEAT 160 192 HAT 5.
 REPEAT 198 230 HAT 6.
 REPEAT 235 268 HAT 7.
 REPEAT 270 305 HAT 8.
 REPEAT 369 407 HAT 9.
 REPEAT 498 530 HAT 10.
 REPEAT 532 566 HAT 11.
 REPEAT 571 605 HAT 12.
 REPEAT 643 677 HAT 13.
 REPEAT 679 713 HAT 14.
 MOD_RES 420 420 N6-acetyllysine.
 MOD_RES 851 851 Phosphoserine.  
Keyword
 Acetylation; Complete proteome; DNA damage; DNA repair; mRNA processing; mRNA splicing; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; Spliceosome; Transcription. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 855 AA 
Protein Sequence
MVVMARLSRP ERPDLVFEEE DLPYEEEIMR NQFSVKCWLR YIEFKQGAPK PRLNQLYERA 60
LKLLPCSYKL WYRYLKARRA QVKHRCVTDP AYEDVNNCHE RAFVFMHKMP RLWLDYCQFL 120
MDQGRVTHTR RTFDRALRAL PITQHSRIWP LYLRFLRSHP LPETAVRGYR RFLKLSPESA 180
EEYIEYLKSS DRLDEAAQRL ATVVNDERFV SKAGKSNYQL WHELCDLISQ NPDKVQSLNV 240
DAIIRGGLTR FTDQLGKLWC SLADYYIRSG HFEKARDVYE EAIRTVMTVR DFTQVFDSYA 300
QFEESMIAAK METASELGRE EEDDVDLELR LARFEQLISR RPLLLNSVLL RQNPHHVHEW 360
HKRVALHQGR PREIINTYTE AVQTVDPFKA TGKPHTLWVA FAKFYEDNGQ LDDARVILEK 420
ATKVNFKQVD DLASVWCQCG ELELRHENYD EALRLLRKAT ALPARRAEYF DGSEPVQNRV 480
YKSLKVWSML ADLEESLGTF QSTKAVYDRI LDLRIATPQI VINYAMFLEE HKYFEESFKA 540
YERGISLFKW PNVSDIWSTY LTKFIARYGG RKLERARDLF EQALDGCPPK YAKTLYLLYA 600
QLEEEWGLAR HAMAVYERAT RAVEPAQQYD MFNIYIKRAA EIYGVTHTRG IYQKAIEVLS 660
DEHAREMCLR FADMECKLGE IDRARAIYSF CSQICDPRTT GAFWQTWKDF EVRHGNEDTI 720
KEMLRIRRSV QATYNTQVNF MASQMLKVSG SATGTVSDLA PGQSGMDDMK LLEQRAEQLA 780
AEAERDQPLR AQSKILFVRS DASREELAEL AQQVNPEEIQ LGEDEDEDEM DLEPNEVRLE 840
QQSVPAAVFG SLKED 855 
Gene Ontology
 GO:0071013; C:catalytic step 2 spliceosome; IDA:UniProtKB.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0001824; P:blastocyst development; IEA:Compara.
 GO:0000398; P:mRNA splicing, via spliceosome; IC:UniProtKB.
 GO:0006351; P:transcription, DNA-dependent; IDA:UniProtKB.
 GO:0006283; P:transcription-coupled nucleotide-excision repair; IDA:UniProtKB. 
Interpro
 IPR003107; HAT.
 IPR013026; TPR-contain_dom.
 IPR011990; TPR-like_helical.
 IPR013105; TPR_2.
 IPR019734; TPR_repeat. 
Pfam
 PF07719; TPR_2 
SMART
 SM00386; HAT 
PROSITE
  
PRINTS