CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-001625
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA-directed RNA polymerase I subunit RPA1 
Protein Synonyms/Alias
 RNA polymerase I subunit A1; A190; DNA-directed RNA polymerase I largest subunit; DNA-directed RNA polymerase I subunit A; RNA polymerase I 194 kDa subunit; RPA194 
Gene Name
 POLR1A 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
5***MLISKNMPWRRLubiquitination[1, 2]
31ELKKLSVKSITNPRYubiquitination[2]
190NVCESKSKLIALFWKubiquitination[2]
222VRKEHNSKLTITFPAubiquitination[2]
238VHRTAGQKDSEPLGIubiquitination[2, 3, 4]
252IEEAQIGKRGYLTPTubiquitination[2, 3, 4]
350ALMAQEQKLPEEVATubiquitination[3]
364TPTTDEEKDSLIAIDubiquitination[3]
413MDKLMMDKYPGIRQIubiquitination[5, 6]
520TQREAVAKQLLTPATubiquitination[2, 4]
536APKPQGTKIVCRHVKubiquitination[2]
543KIVCRHVKNGDILLLubiquitination[2]
573ARILPEEKVLRLHYAubiquitination[2, 5, 6]
583RLHYANCKAYNADFDubiquitination[2]
664VYRGLTDKVGRVKLLubiquitination[2]
669TDKVGRVKLLSPSILubiquitination[2]
677LLSPSILKPFPLWTGubiquitination[1, 2, 4]
714GKAKITGKAWVKETPubiquitination[2]
718ITGKAWVKETPRSVPubiquitination[2]
805GVEDILVKPKADVKRubiquitination[2, 3]
807EDILVKPKADVKRQRubiquitination[2]
845SYDEVRGKWQDAHLGubiquitination[2, 3]
853WQDAHLGKDQRDFNMubiquitination[2]
864DFNMIDLKFKEEVNHubiquitination[2, 3]
866NMIDLKFKEEVNHYSubiquitination[2]
878HYSNEINKACMPFGLubiquitination[2]
933PPLMASGKSLPCFEPubiquitination[2]
960GRFLTGIKPPEFFFHubiquitination[2]
981GLVDTAVKTSRSGYLubiquitination[1, 2, 3]
1028EDGLDIPKTQFLQPKubiquitination[3]
1078AIKKWQSKHPNTLLRubiquitination[2]
1095AFLSYSQKIQEAVKAubiquitination[2]
1101QKIQEAVKALKLESEubiquitination[2, 3]
1104QEAVKALKLESENRNubiquitination[1, 2]
1180EWAAQTEKSYEKSELubiquitination[2, 3, 4]
1184QTEKSYEKSELSLDRubiquitination[2, 3]
1199LRTLLQLKWQRSLCEubiquitination[2, 3]
1273VPVLNTKKALKRVKSubiquitination[2]
1311CMEEKQNKFQVYQLRubiquitination[2]
1331HAYYQQEKCLRPEDIubiquitination[2]
1356LLMESIKKKNNKASAubiquitination[2]
1360SIKKKNNKASAFRNVubiquitination[2]
1416DADASDAKRKEKQEEubiquitination[3]
1485ALLTQPRKPTHSQEPubiquitination[2]
1574TTNNKNEKELVLNTEubiquitination[3]
1704SACLVVGKVVRGGTGubiquitination[2, 5, 6]
1716GTGLFELKQPLR***ubiquitination[2, 3, 4]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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] 
Functional Description
 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol I. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition (By similarity). 
Sequence Annotation
 REGION 961 973 Bridging helix (By similarity).
 METAL 64 64 Zinc (By similarity).
 METAL 67 67 Zinc (By similarity).
 METAL 74 74 Zinc (By similarity).
 METAL 77 77 Zinc (By similarity).
 METAL 588 588 Magnesium; catalytic (By similarity).
 METAL 590 590 Magnesium; catalytic (By similarity).
 METAL 592 592 Magnesium; catalytic (By similarity).
 MOD_RES 1386 1386 Phosphoserine.  
Keyword
 Complete proteome; DNA-directed RNA polymerase; Magnesium; Metal-binding; Nucleotidyltransferase; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Transcription; Transferase; Zinc. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1720 AA 
Protein Sequence
MLISKNMPWR RLQGISFGMY SAEELKKLSV KSITNPRYLD SLGNPSANGL YDLALGPADS 60
KEVCSTCVQD FSNCSGHLGH IELPLTVYNP LLFDKLYLLL RGSCLNCHML TCPRAVIHLL 120
LCQLRVLEVG ALQAVYELER ILNRFLEENP DPSASEIREE LEQYTTEIVQ NNLLGSQGAH 180
VKNVCESKSK LIALFWKAHM NAKRCPHCKT GRSVVRKEHN SKLTITFPAM VHRTAGQKDS 240
EPLGIEEAQI GKRGYLTPTS AREHLSALWK NEGFFLNYLF SGMDDDGMES RFNPSVFFLD 300
FLVVPPSRYR PVSRLGDQMF TNGQTVNLQA VMKDVVLIRK LLALMAQEQK LPEEVATPTT 360
DEEKDSLIAI DRSFLSTLPG QSLIDKLYNI WIRLQSHVNI VFDSEMDKLM MDKYPGIRQI 420
LEKKEGLFRK HMMGKRVDYA ARSVICPDMY INTNEIGIPM VFATKLTYPQ PVTPWNVQEL 480
RQAVINGPNV HPGASMVINE DGSRTALSAV DMTQREAVAK QLLTPATGAP KPQGTKIVCR 540
HVKNGDILLL NRQPTLHRPS IQAHRARILP EEKVLRLHYA NCKAYNADFD GDEMNAHFPQ 600
SELGRAEAYV LACTDQQYLV PKDGQPLAGL IQDHMVSGAS MTTRGCFFTR EHYMELVYRG 660
LTDKVGRVKL LSPSILKPFP LWTGKQVVST LLINIIPEDH IPLNLSGKAK ITGKAWVKET 720
PRSVPGFNPD SMCESQVIIR EGELLCGVLD KAHYGSSAYG LVHCCYEIYG GETSGKVLTC 780
LARLFTAYLQ LYRGFTLGVE DILVKPKADV KRQRIIEEST HCGPQAVRAA LNLPEAASYD 840
EVRGKWQDAH LGKDQRDFNM IDLKFKEEVN HYSNEINKAC MPFGLHRQFP ENSLQMMVQS 900
GAKGSTVNTM QISCLLGQIE LEGRRPPLMA SGKSLPCFEP YEFTPRAGGF VTGRFLTGIK 960
PPEFFFHCMA GREGLVDTAV KTSRSGYLQR CIIKHLEGLV VQYDLTVRDS DGSVVQFLYG 1020
EDGLDIPKTQ FLQPKQFPFL ASNYEVIMKS QHLHEVLSRA DPKKALHHFR AIKKWQSKHP 1080
NTLLRRGAFL SYSQKIQEAV KALKLESENR NGRSPGTQEM LRMWYELDEE SRRKYQKKAA 1140
ACPDPSLSVW RPDIYFASVS ETFETKVDDY SQEWAAQTEK SYEKSELSLD RLRTLLQLKW 1200
QRSLCEPGEA VGLLAAQSIG EPSTQMTLNT FHFAGRGEMN VTLGIPRLRE ILMVASANIK 1260
TPMMSVPVLN TKKALKRVKS LKKQLTRVCL GEVLQKIDVQ ESFCMEEKQN KFQVYQLRFQ 1320
FLPHAYYQQE KCLRPEDILR FMETRFFKLL MESIKKKNNK ASAFRNVNTR RATQRDLDNA 1380
GELGRSRGEQ EGDEEEEGHI VDAEAEEGDA DASDAKRKEK QEEEVDYESE EEEEREGEEN 1440
DDEDMQEERN PHREGARKTQ EQDEEVGLGT EEDPSLPALL TQPRKPTHSQ EPQGPEAMER 1500
RVQAVREIHP FIDDYQYDTE ESLWCQVTVK LPLMKINFDM SSLVVSLAHG AVIYATKGIT 1560
RCLLNETTNN KNEKELVLNT EGINLPELFK YAEVLDLRRL YSNDIHAIAN TYGIEAALRV 1620
IEKEIKDVFA VYGIAVDPRH LSLVADYMCF EGVYKPLNRF GIRSNSSPLQ QMTFETSFQF 1680
LKQATMLGSH DELRSPSACL VVGKVVRGGT GLFELKQPLR 1720 
Gene Ontology
 GO:0005736; C:DNA-directed RNA polymerase I complex; NAS:UniProtKB.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0003677; F:DNA binding; IEA:InterPro.
 GO:0003899; F:DNA-directed RNA polymerase activity; IEA:UniProtKB-KW.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0006363; P:termination of RNA polymerase I transcription; TAS:Reactome.
 GO:0006362; P:transcription elongation from RNA polymerase I promoter; TAS:Reactome.
 GO:0006361; P:transcription initiation from RNA polymerase I promoter; TAS:Reactome. 
Interpro
 IPR009010; Asp_de-COase-like_dom.
 IPR015699; DNA-dir_RNA_pol1_lsu.
 IPR000722; RNA_pol_asu.
 IPR006592; RNA_pol_N.
 IPR007080; RNA_pol_Rpb1_1.
 IPR007066; RNA_pol_Rpb1_3.
 IPR007083; RNA_pol_Rpb1_4.
 IPR007081; RNA_pol_Rpb1_5. 
Pfam
 PF04997; RNA_pol_Rpb1_1
 PF00623; RNA_pol_Rpb1_2
 PF04983; RNA_pol_Rpb1_3
 PF05000; RNA_pol_Rpb1_4
 PF04998; RNA_pol_Rpb1_5 
SMART
 SM00663; RPOLA_N 
PROSITE
  
PRINTS