dbPAF Protein Information


Tag Content
dbPAF ID dbPAF-0004122
Uniprot Accession P04050; RPB1_YEAST; D6VRK8; Q12364; Q92315;
Genbank Protein ID NP_010141.1;
Genbank Nucleotide ID NM_001180200.1;
Protein Name DNA-directed RNA polymerase II subunit RPB1
Protein Synonyms/Alias
Gene Name RPO21
Gene Synonyms/Alias RPB1;RPB220;SUA8;YDL140C;D2150;
Organism Saccharomyces cerevisiae (strain ATCC 204508 / S288c)(Baker's yeast)
NCBI Taxa ID 559292
Functional Description
(View all)
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single-stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II 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. In elongating Pol II, the lid loop (RPB1) appears to act as a wedge to drive apart the DNA and RNA strands at the upstream end of the transcription bubble and guide the RNA strand toward the RNA exit groove located near the base of the largely unstructured CTD domain of RPB1. The rudder loop (RPB1) interacts with single-stranded DNA after separation from the RNA strand, likely preventing reassociation with the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and portions of RBP1. The jaws are thought to grab the incoming DNA template, mainly by RPB5 direct contacts to DNA.
Phosphorylation Sites
dbPAF PTMs: 36 (View all)
PositionPeptidesSourceReferences ( PMIDs )
449VLFNRQPSLHKMSMMcurated24961812
595LQRFDEGTTLLSPKDPhosphoGRID 2.0;curated21177495; 22817900
596QRFDEGTTLLSPKDNPhosphoGRID 2.0;curated21177495; 22817900
599DEGTTLLSPKDNGMLPhosphoGRID 2.0;curated21177495; 22817900; 25315811
621FGVVEKKTVGSSNGGdbPTM 3.0;PhosphoGRID 2.0;curated17563356; 16381945; 23193290; 22817900
793HFSKDDYSPESKGFVcurated25315811
933QVLLDEEYKQLVKDRcurated22817900
1293KYDRKVPSPTGEYVKdbPTM 3.0;PhosphoGRID 2.0;PhosphoPep 2.0;SysPTM 2.0;curated17330950; 16381945; 23193290; 21126336; 19060867; 19366988;
1295DRKVPSPTGEYVKEPcurated25315811
1460YMPEQKITEIEDGQDcurated22817900
1471DGQDGGVTPYSNESGdbPTM 3.0;PhosphoGRID 2.0;SysPTM 2.0;UniProt;curated18407956; 16381945; 23193290; 20489023; 19366988; 26040289;
1473QDGGVTPYSNESGLVdbPTM 3.0;PhosphoGRID 2.0;SysPTM 2.0;curated18407956; 16381945; 23193290; 19366988
1543GVSSPGFSPTSPTYSPhosphoGRID 2.020818391; 9237170; 11018013; 10594013; 12972617; 11751637
1546SPGFSPTSPTYSPTSPhosphoGRID 2.020818391; 9237170; 11018013; 11390638; 12972617; 10594013
1550SPTSPTYSPTSPAYSPhosphoGRID 2.020818391; 9237170; 11018013; 10594013; 12972617; 11751637
1553SPTYSPTSPAYSPTSPhosphoGRID 2.020818391; 9237170; 11018013; 11390638; 12972617; 10594013
1557SPTSPAYSPTSPSYSPhosphoGRID 2.020818391; 9237170; 11018013; 10594013; 12972617; 11751637
1560SPAYSPTSPSYSPTSPhosphoGRID 2.020818391; 9237170; 11018013; 11390638; 12972617; 10594013
1562AYSPTSPSYSPTSPSPhosphoGRID 2.020818391; 20835241; 19679665; 19450536
1564SPTSPSYSPTSPSYSPhosphoGRID 2.020818391; 9237170; 11018013; 10594013; 12972617; 11751637
Sequence
(Fasta)
MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS 60
IDRNLKCQTC QEGMNECPGH FGHIDLAKPV FHVGFIAKIK KVCECVCMHC GKLLLDEHNE 120
LMRQALAIKD SKKRFAAIWT LCKTKMVCET DVPSEDDPTQ LVSRGGCGNT QPTIRKDGLK 180
LVGSWKKDRA TGDADEPELR VLSTEEILNI FKHISVKDFT SLGFNEVFSR PEWMILTCLP 240
VPPPPVRPSI SFNESQRGED DLTFKLADIL KANISLETLE HNGAPHHAIE EAESLLQFHV 300
ATYMDNDIAG QPQALQKSGR PVKSIRARLK GKEGRIRGNL MGKRVDFSAR TVISGDPNLE 360
LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP GAKYVIRDSG DRIDLRYSKR 420
AGDIQLQYGW KVERHIMDND PVLFNRQPSL HKMSMMAHRV KVIPYSTFRL NLSVTSPYNA 480
DFDGDEMNLH VPQSEETRAE LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKLTLRDTF 540
IELDQVLNML YWVPDWDGVI PTPAIIKPKP LWSGKQILSV AIPNGIHLQR FDEGTTLLSP 600
KDNGMLIIDG QIIFGVVEKK TVGSSNGGLI HVVTREKGPQ VCAKLFGNIQ KVVNFWLLHN 660
GFSTGIGDTI ADGPTMREIT ETIAEAKKKV LDVTKEAQAN LLTAKHGMTL RESFEDNVVR 720
FLNEARDKAG RLAEVNLKDL NNVKQMVMAG SKGSFINIAQ MSACVGQQSV EGKRIAFGFV 780
DRTLPHFSKD DYSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR 840
LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGSD AAFEKRYRVD 900
LLNTDHTLDP SLLESGSEIL GDLKLQVLLD EEYKQLVKDR KFLREVFVDG EANWPLPVNI 960
RRIIQNAQQT FHIDHTKPSD LTIKDIVLGV KDLQENLLVL RGKNEIIQNA QRDAVTLFCC 1020
LLRSRLATRR VLQEYRLTKQ AFDWVLSNIE AQFLRSVVHP GEMVGVLAAQ SIGEPATQMT 1080
LNTFHFAGVA SKKVTSGVPR LKEILNVAKN MKTPSLTVYL EPGHAADQEQ AKLIRSAIEH 1140
TTLKSVTIAS EIYYDPDPRS TVIPEDEEII QLHFSLLDEE AEQSFDQQSP WLLRLELDRA 1200
AMNDKDLTMG QVGERIKQTF KNDLFVIWSE DNDEKLIIRC RVVRPKSLDA ETEAEEDHML 1260
KKIENTMLEN ITLRGVENIE RVVMMKYDRK VPSPTGEYVK EPEWVLETDG VNLSEVMTVP 1320
GIDPTRIYTN SFIDIMEVLG IEAGRAALYK EVYNVIASDG SYVNYRHMAL LVDVMTTQGG 1380
LTSVTRHGFN RSNTGALMRC SFEETVEILF EAGASAELDD CRGVSENVIL GQMAPIGTGA 1440
FDVMIDEESL VKYMPEQKIT EIEDGQDGGV TPYSNESGLV NADLDVKDEL MFSPLVDSGS 1500
NDAMAGGFTA YGGADYGEAT SPFGAYGEAP TSPGFGVSSP GFSPTSPTYS PTSPAYSPTS 1560
PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS 1620
PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP 1680
SYSPTSPSYS PTSPNYSPTS PSYSPTSPGY SPGSPAYSPK QDEQKHNENE NSR 1734
Keyword

KW-0002--3D-structure
KW-0181--Complete proteome
KW-0238--DNA-binding
KW-0240--DNA-directed RNA polymerase
KW-1017--Isopeptide bond
KW-0460--Magnesium
KW-0479--Metal-binding
KW-0548--Nucleotidyltransferase
KW-0539--Nucleus
KW-0597--Phosphoprotein
KW-1185--Reference proteome
KW-0677--Repeat
KW-0804--Transcription
KW-0808--Transferase
KW-0832--Ubl conjugation
KW-0862--Zinc

Interpro

IPR000722--RNA_pol_asu
IPR000684--RNA_pol_II_repeat_euk
IPR006592--RNA_pol_N
IPR007080--RNA_pol_Rpb1_1
IPR007066--RNA_pol_Rpb1_3
IPR007083--RNA_pol_Rpb1_4
IPR007081--RNA_pol_Rpb1_5
IPR007075--RNA_pol_Rpb1_6
IPR007073--RNA_pol_Rpb1_7

PROSITE

PS00115--RNA_POL_II_REPEAT

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
PF04992--RNA_pol_Rpb1_6
PF04990--RNA_pol_Rpb1_7
PF05001--RNA_pol_Rpb1_R

Gene Ontology

GO:0005665--C:DNA-directed RNA polymerase II, core complex
GO:0005634--C:nucleus
GO:0003677--F:DNA binding
GO:0003899--F:DNA-directed RNA polymerase activity
GO:0046872--F:metal ion binding
GO:0006366--P:transcription from RNA polymerase II promoter
GO:0001172--P:transcription, RNA-templated
GO:0019985--P:translesion synthesis