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DNA-directed RNA polymerase II subunit RPB
Known also as: DNA-directed RNA polymerase II subunit A, DNA-directed RNA polymerase III largest subunit, RNA polymerase II subunit B1
Known abbreviations: RPB1, hRPB220, hsRPB1, POLR2, POLR2A, POLRA, RPBh1, RpIILS, RPO2, RPOL2
Yeast homolog: RPB1
Protein
Structures Models Domains Secondary structure NTD, CTD |
Top 3 models:
 |  |  |
| Template: 1twf, chain A Method: hhsearch Fragment: 3-990 | Template: 3h0g, chain A Method: hhsearch Fragment: 3-990 | Template: 2gho, chain D Method: ffas Fragment: 16-987 |
| Sequence length: | 1970 aa |
| Molecular weight: | 217.176 kDa |
| Isoelectric point: | 7.1 |
Sequence:
1........10........20........30........40........50........60........70........80........90........100.......110.......120.......130
MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDIL
AKSKGQPKKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSV
RPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTF
AEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAM
VPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAG
SLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKIN
ISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATLK
PSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLL
FNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVT
ANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQG
IEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKC
SFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTGMFFGSAPSPMGGISPAMTPWNQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPG
YSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAYEPRSPGGYTPQSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP
SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTSPSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTP
SSPSYSPSSPSYSPASPKYTPTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPT
SPTYSLTSPAISPDDSDEEN
Enzyme
EC number: 2.7.7.6
Name: DNA-directed RNA polymerase
Reaction: Nucleoside triphosphate + RNA(n) <=> diphosphate + RNA(n+1)
EC number: 2.7.7.48
Name: RNA-directed RNA polymerase
Reaction: Nucleoside triphosphate + RNA(n) <=> diphosphate + RNA(n+1)
Gene location: 17p13.1
Summary
The C teminal domain (CTD) od RNA polymerase II is made up of 52 heptapeptide repeats in humans and 26 repeats in yeast with a consensus sequence of YSPTSPS for each repeat. The repeated serine residues within the CTD are susceptible to phosphorylation. The CTD is not observed in the structure of yeast PolII, suggesting that it may be flexible. The structure of the CTD peptide depends on interaction partner and modification state. When it is phosphorylated at serine the CTD peptide assumed the conformation of a ?-turn, while CTD peptides have also been observed in more extended conformations. The variety of CTD conformations suggests that the CTD may not form a single basal structure and it is intrinsically unstructured region. PolII was identified in 3?-end processing because transiently transfected cells with CTD truncations exhibit inefficient polyadenylation.
Both mammalian and yeast CTD bind CPSF-160 (Cft1p/Yhh1p). Additionally, the mammalian CTD binds CstF-50 [85]. Protein binding generally increases upon phosphorylation of the CTD, and 3?-end processing is stimulated in vitro by phosphorylated CTD.
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. It is composed of mobile elements that move relative to each other. RPB1 is part of the core element with the central large cleft, the clamp element that moves to open and close the cleft and the jaws that are thought to grab the incoming DNA template. At the start of transcription, a single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol II. 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. During transcription elongation, Pol II moves on the template as the transcript elongates. 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. Acts as a RNA-dependent RNA polymerase when associated with small delta antigen of Hepatitis delta virus, acting both as a replicate and transcriptase for the viral RNA circular genome.
Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.
The tandem 7 residues repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II. Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapeptide repeat and is mediated, at least, by CDK7 and CDK9. CDK7 phosphorylation of POLR2A associated with DNA promotes transcription initiation by triggering dissociation from DNA. Phosphorylation also takes place at 'Ser-7' of the heptapepdtide repeat, which is required for efficient transcription of snRNA genes and processing of the transcripts. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphatases, and a 'CTD code' that specifies the position of Pol II within the transcription cycle has been proposed.
Dephosphorylated by the protein phosphatase CTDSP1.
Ubiquitinated by WWP2 leading to proteasomal degradation.
Methylated at Arg-1810 by CARM1. Methylation occurs only when the CTD is hypophosphorylated, and phosphorylation at Ser-1805 and Ser-1808 prevent methylation (in vitro). It is assumed that methylation occurs prior to phosphorylation and transcription initiation. CTD methylation may facilitate the expression of select RNAs.
See this protein in other databases:
Literature:
- Egloff S, Murphy S. Cracking the RNA polymerase II CTD code. Trends Genet 2008 24(6):280-8, doi: 10.1016/ j.tig.2008.03.008, PMID: 18457900.
- Bartkowiak B, Mackellar AL, Greenleaf AL et al. Updating the CTD Story: From Tail to Epic. Genet Res Int 2011 2011:623718, doi: 10.4061/2011/623718, PMID: 22567360.
- Zhang DW, Rodriguez-Molina JB, Tietjen JR et al. Emerging Views on the CTD Code. Genet Res Int 2012 2012:347214, doi: 10.1155/2012/347214, PMID: 22567385.
- Egloff S, Dienstbier M, Murphy S et al. Updating the RNA polymerase CTD code: adding gene-specific layers. Trends Genet 2012 28(7):333-41, doi: 10.1016/j.tig.2012.03.007, PMID: 22622228.
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