CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-006536
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 RNA polymerase II degradation factor 1 
Protein Synonyms/Alias
 RRM3-interacting protein 1 
Gene Name
 DEF1 
Gene Synonyms/Alias
 RIP1; VID31; YKL054C; YKL308 
Created Date
 July 27, 2013 
Organism
 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 
NCBI Taxa ID
 559292 
Lysine Modification
Position
Peptide
Type
References
115SNSFTSTKHNSSNNYubiquitination[1]
141PRAHTTGKHVNLDKGacetylation[2]
147GKHVNLDKGKHVPSKubiquitination[1]
196QGQQAQEKNQEKEQEubiquitination[3]
Reference
 [1] Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
 Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.
 Nat Methods. 2013 Jul;10(7):676-82. [PMID: 23749301]
 [2] mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases.
 Mitchell L, Huard S, Cotrut M, Pourhanifeh-Lemeri R, Steunou AL, Hamza A, Lambert JP, Zhou H, Ning Z, Basu A, Côté J, Figeys DA, Baetz K.
 Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):E1641-50. [PMID: 23572591]
 [3] Sites of ubiquitin attachment in Saccharomyces cerevisiae.
 Starita LM, Lo RS, Eng JK, von Haller PD, Fields S.
 Proteomics. 2012 Jan;12(2):236-40. [PMID: 22106047] 
Functional Description
 RNA polymerase II degradation factor recruits the ubiquitination machinery to the RNA polymerase II for polyubiquitination, removal and degradation, when RAD26 fails to efficiently displace stalled RNA polymerase II. Also involved in telomere length regulation. 
Sequence Annotation
 DOMAIN 21 63 CUE.
 MOD_RES 260 260 Phosphoserine.
 MOD_RES 273 273 Phosphoserine.
 MOD_RES 307 307 Phosphoserine.
 MOD_RES 338 338 Phosphothreonine.
 MOD_RES 646 646 Phosphoserine.  
Keyword
 Chromosome; Complete proteome; DNA damage; DNA repair; DNA-binding; Nucleus; Phosphoprotein; Reference proteome; Telomere; Ubl conjugation pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 738 AA 
Protein Sequence
MSTQFRKSNH NSHSSKKLNP ALKSKIDTLT ELFPDWTSDD LIDIVQEYDD LETIIDKITS 60
GAVTRWDEVK KPAKKEKYEK KEQQHSYVPQ QHLPNPEDDI TYKSSNNSNS FTSTKHNSSN 120
NYTQARNKKK VQTPRAHTTG KHVNLDKGKH VPSKPVSNTT SWAAAVSVDT KHDVPQDSND 180
NNNEELEAQG QQAQEKNQEK EQEEQQQQEG HNNKEEHKQI EQPSLSSKKT TSRTSASQPK 240
KMSWAAIATP KPKAVKKTES PLENVAELKK EISDIKKDDQ KSEASEEKVN EQETSAQEQE 300
EETAEPSEEN EDRVPEVDGE EVQEEAEKKE QVKEEEQTAE ELEQEQDNVA APEEEVTVVE 360
EKVEISAVIS EPPEDQANTV PQPQQQSQQP QQPQQPQQPQ QPQQPQQQQQ PQQPQQPQQQ 420
LQQQQQQQQQ PVQAQAQAQE EQLSQNYYTQ QQQQQYAQQQ HQLQQQYLSQ QQQYAQQQQQ 480
HPQPQSQQPQ SQQSPQSQKQ GNNVAAQQYY MYQNQFPGYS YPGMFDSQGY AYGQQYQQLA 540
QNNAQTSGNA NQYNFQQGYG QAGANTAAAN LTSAAAAAAA SPATAHAQPQ QQQPYGGSFM 600
PYYAHFYQQS FPYGQPQYGV AGQYPYQLPK NNYNYYQTQN GQEQQSPNQG VAQHSEDSQQ 660
KQSQQQQQQQ PQGQPQPEVQ MQNGQPVNPQ QQMQFQQYYQ FQQQQQQAAA AAAAAAQQGV 720
PYGYNGYDYN SKNSRGFY 738 
Gene Ontology
 GO:0000781; C:chromosome, telomeric region; IEA:UniProtKB-SubCell.
 GO:0005634; C:nucleus; IMP:SGD.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0000723; P:telomere maintenance; IMP:SGD.
 GO:0006283; P:transcription-coupled nucleotide-excision repair; IGI:SGD.
 GO:0006511; P:ubiquitin-dependent protein catabolic process; IDA:SGD. 
Interpro
 IPR003892; CUE. 
Pfam
 PF02845; CUE 
SMART
  
PROSITE
 PS51140; CUE 
PRINTS