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Protein

DNA-directed RNA polymerase II subunit RPB1

Gene

ama-1

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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 (By similarity). Involved in the transcription of several genes including those involved in embryogenesis (PubMed:14726532, PubMed:27541139).By similarity2 Publications

Miscellaneous

The binding of ribonucleoside triphosphate to the RNA polymerase II transcribing complex probably involves a two-step mechanism. The initial binding seems to occur at the entry (E) site and involves a magnesium ion temporarily coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits. The ribonucleoside triphosphate is transferred by a rotation to the nucleotide addition (A) site for pairing with the template DNA. The catalytic A site involves three conserved aspartate residues of the RNA Pol II largest subunit which permanently coordinate a second magnesium ion.

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi66Zinc 1By similarity1
Metal bindingi69Zinc 1By similarity1
Metal bindingi76Zinc 1By similarity1
Metal bindingi79Zinc 1By similarity1
Metal bindingi106Zinc 2By similarity1
Metal bindingi109Zinc 2By similarity1
Metal bindingi149Zinc 2By similarity1
Metal bindingi177Zinc 2By similarity1
Metal bindingi489Magnesium 1; catalyticBy similarity1
Metal bindingi489Magnesium 2; shared with RPB2By similarity1
Metal bindingi491Magnesium 1; catalyticBy similarity1
Metal bindingi491Magnesium 2; shared with RPB2By similarity1
Metal bindingi493Magnesium 1; catalyticBy similarity1

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • DNA-directed 5'-3' RNA polymerase activity Source: WormBase
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • embryo development ending in birth or egg hatching Source: WormBase
  • gastrulation Source: WormBase
  • mRNA transcription by RNA polymerase II Source: WormBase
  • positive regulation of gastrulation Source: UniProtKB
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • transcription, DNA-templated Source: WormBase

Keywordsi

Molecular functionDNA-binding, Nucleotidyltransferase, Transferase
Biological processTranscription
LigandMagnesium, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB1 (EC:2.7.7.6)
Short name:
RNA polymerase II subunit B1
Alternative name(s):
DNA-directed RNA polymerase III largest subunit
Gene namesi
Name:ama-1Imported
Synonyms:rpb-1Imported
ORF Names:F36A4.7Imported
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome IV

Organism-specific databases

WormBaseiF36A4.7 ; CE46402 ; WBGene00000123 ; ama-1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Chromosome, DNA-directed RNA polymerase, Nucleus

Pathology & Biotechi

Disruption phenotypei

RNAi-mediated knockdown results in embryonic arrest at the 100-cell stage and prevents the embryonic transcription of several genes (PubMed:14726532). Surviving embryos exhibit gastrulation defects with decreased expression of genes involved in gastrulation (PubMed:27541139).2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000739351 – 1856DNA-directed RNA polymerase II subunit RPB1Add BLAST1856

Post-translational modificationi

The tandem 7 residues repeats in the C-terminal domain (CTD) can be highly phosphorylated. The phosphorylation activates Pol II (By similarity). Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the heptapeptide repeat and starts at the 3- to 4-cell embryonic stage (PubMed:14726532, PubMed:17291483). This phosphorylation also occurs in the early stages of oocyte development and is not detected in oocytes arrested at the meiotic diakinesis stage (PubMed:17291483). In the somatic lineage, phosphorylation at 'Ser-2' is mediated by cdk-12 downstream of cdk-9 whereas in the germline lineage cdk-12 phosphorylates 'Ser-2' independently of cdk-9 (PubMed:23903194). Phosphorylation is likely mediated by cdk-7 (PubMed:11960010). May be dephosphorylated by fcp-1 in diakinetic oocytes and in 1-cell and 2-cell embryos (PubMed:17291483). The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphatase, and a 'CTD code' that specifies the position of Pol II within the transcription cycle has been proposed (By similarity).1 PublicationBy similarity3 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP16356
PaxDbiP16356
PeptideAtlasiP16356
PRIDEiP16356

PTM databases

iPTMnetiP16356

Expressioni

Developmental stagei

Expressed in embryo. During embryonic development, the form phosphorylated at 'Ser-2' of the C-terminal heptapeptide repeats is present only in transcriptionally active somatic cells.1 Publication

Gene expression databases

BgeeiWBGene00000123

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits (By similarity). Interacts with sig-7 (PubMed:27541139).By similarity1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
mdt-6Q9N3372EBI-1533906,EBI-1533827

Protein-protein interaction databases

IntActiP16356, 4 interactors
STRINGi6239.F36A4.7.2

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati1593 – 159917
Repeati1600 – 160627
Repeati1616 – 162237
Repeati1623 – 162947
Repeati1630 – 163657
Repeati1637 – 164367
Repeati1644 – 165077
Repeati1651 – 165787
Repeati1658 – 166497
Repeati1665 – 1671107
Repeati1672 – 1678117
Repeati1679 – 1685127
Repeati1686 – 1692137
Repeati1693 – 1699147
Repeati1700 – 1706157
Repeati1707 – 1713167
Repeati1720 – 1726177
Repeati1727 – 1733187
Repeati1734 – 1740197
Repeati1741 – 1747207
Repeati1748 – 1754217
Repeati1755 – 1761227
Repeati1769 – 1775237
Repeati1782 – 1788247
Repeati1789 – 1795257
Repeati1796 – 1802267
Repeati1803 – 1809277
Repeati1810 – 181628; approximate7

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni256 – 268Lid loopAdd BLAST13
Regioni314 – 331Rudder loopAdd BLAST18
Regioni827 – 839Bridging helixAdd BLAST13
Regioni1593 – 1816C-terminal domain (CTD); 28 X 7 AA approximate tandem repeats of Y-[ST]-P-[ST]-S-P-[AGKNQRST]Add BLAST224

Domaini

The C-terminal domain (CTD) serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.Curated

Sequence similaritiesi

Belongs to the RNA polymerase beta' chain family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0260 Eukaryota
COG0086 LUCA
GeneTreeiENSGT00920000149105
HOGENOMiHOG000222975
InParanoidiP16356
KOiK03006
OMAiMPDFDPT
OrthoDBiEOG091G00CH

Family and domain databases

Gene3Di1.10.132.30, 1 hit
3.30.1360.140, 1 hit
InterProiView protein in 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
IPR038593 RNA_pol_Rpb1_7_sf
IPR038120 Rpb1_funnel_sf
PfamiView protein in Pfam
PF04997 RNA_pol_Rpb1_1, 1 hit
PF00623 RNA_pol_Rpb1_2, 1 hit
PF04983 RNA_pol_Rpb1_3, 1 hit
PF05000 RNA_pol_Rpb1_4, 1 hit
PF04998 RNA_pol_Rpb1_5, 1 hit
PF04992 RNA_pol_Rpb1_6, 1 hit
PF04990 RNA_pol_Rpb1_7, 1 hit
PF05001 RNA_pol_Rpb1_R, 20 hits
SMARTiView protein in SMART
SM00663 RPOLA_N, 1 hit
PROSITEiView protein in PROSITE
PS00115 RNA_POL_II_REPEAT, 26 hits

Sequencei

Sequence statusi: Complete.

P16356-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALVGVDFQA PLRIVSRVQF GILGPEEIKR MSVAHVEFPE VYENGKPKLG
60 70 80 90 100
GLMDPRQGVI DRRGRCMTCA GNLTDCPGHF GHLELAKPVF HIGFLTKTLK
110 120 130 140 150
ILRCVCFYCG RLLIDKSAPR VLEILKKTGT NSKKRLTMIY DLCKAKSVCE
160 170 180 190 200
GAAEKEEGMP DDPDDPMNDG KKVAGGCGRY QPSYRRVGID INAEWKKNVN
210 220 230 240 250
EDTQERKIML TAERVLEVFQ QITDEDILVI GMDPQFARPE WMICTVLPVP
260 270 280 290 300
PLAVRPAVVT FGSAKNQDDL THKLSDIIKT NQQLQRNEAN GAAAHVLTDD
310 320 330 340 350
VRLLQFHVAT LVDNCIPGLP TATQKGGRPL KSIKQRLKGK EGRIRGNLMG
360 370 380 390 400
KRVDFSARTV ITADPNLPID TVGVPRTIAQ NLTFPEIVTP FNVDKLQELV
410 420 430 440 450
NRGDTQYPGA KYIIRENGAR VDLRYHPRAA DLHLQPGYRV ERHMKDGDII
460 470 480 490 500
VFNRQPTLHK MSMMGHRVKI LPWSTFRMNL SVTSPYNADF DGDEMNLHLP
510 520 530 540 550
QSLETRAEIE EIAMVPRQLI TPQANKPVMG IVQDTLCAVR MMTKRDVFID
560 570 580 590 600
WPFMMDLLMY LPTWDGKVPQ PAILKPKPLW TGKQVFSLII PGNVNVLRTH
610 620 630 640 650
STHPDSEDSG PYKWISPGDT KVIIEHGELL SGIVCSKTVG KSAGNLLHVV
660 670 680 690 700
TLELGYEIAA NFYSHIQTVI NAWLIREGHT IGIGDTIADQ ATYLDIQNTI
710 720 730 740 750
RKAKQDVVDV IEKAHNDDLE PTPGNTLRQT FENKVNQILN DARDRTGSSA
760 770 780 790 800
QKSLSEFNNF KSMVVSGSKG SKINISQVIA CVGQQNVEGK RIPFGFRHRT
810 820 830 840 850
LPHFIKDDYG PESKGFVENS YLAGLTPSEF FFHAMGGREG LIDTAVKTAE
860 870 880 890 900
TGYIQRRLIK AMESVMVNYD GTVRNSLAQM VQLRYGEDGL DGMWVENQNM
910 920 930 940 950
PTMKPNNAVF ERDFRMDLTD NKFLRKNYSE DVVREIQESE DGISLVESEW
960 970 980 990 1000
SQLEEDRRLL RKIFPRGDAK IVLPCNLQRL IWNAQKIFKV DLRKPVNLSP
1010 1020 1030 1040 1050
LHVISGVREL SKKLIIVSGN DEISKQAQYN ATLLMNILLR STLCTKNMCT
1060 1070 1080 1090 1100
KSKLNSEAFD WLLGEIESRF QQAIAQPGEM VGALAAQSLG EPATQMTLNT
1110 1120 1130 1140 1150
FHYAGVSAKN VTLGVPRLKE IINVSKTLKT PSLTVFLTGA AAKDPEKAKD
1160 1170 1180 1190 1200
VLCKLEHTTL KKVTCNTAIY YDPDPKNTVI AEDEEWVSIF YEMPDHDLSR
1210 1220 1230 1240 1250
TSPWLLRIEL DRKRMVDKKL TMEMIADRIH GGFGNDVHTI YTDDNAEKLV
1260 1270 1280 1290 1300
FRLRIAGEDK GEAQEEQVDK MEDDVFLRCI EANMLSDLTL QGIPAISKVY
1310 1320 1330 1340 1350
MNQPNTDDKK RIIITPEGGF KSVADWILET DGTALLRVLS ERQIDPVRTT
1360 1370 1380 1390 1400
SNDICEIFEV LGIEAVRKAI EREMDNVISF DGSYVNYRHL ALLCDVMTAK
1410 1420 1430 1440 1450
GHLMAITRHG INRQEVGALM RCSFEETVDI LMEAAVHAEE DPVKGVSENI
1460 1470 1480 1490 1500
MLGQLARCGT GCFDLVLDVE KCKYGMEIPQ NVVMGGGFYG SFAGSPSNRE
1510 1520 1530 1540 1550
FSPAHSPWNS GVTPTYAGAA WSPTTGGMSP GAGFSPAGNT DGGASPFNEG
1560 1570 1580 1590 1600
GWSPASPGDP LGALSPRTPS YGGMSPGVYS PSSPQFSMTS PHYSPTSPSY
1610 1620 1630 1640 1650
SPTSPAAGQS PVSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS
1660 1670 1680 1690 1700
YSPTSPSYSP SSPSYSPSSP SYSPSSPRYS PTSPTYSPTS PTYSPTSPTY
1710 1720 1730 1740 1750
SPTSPTYSPT SPSYESGGGY SPSSPKYSPS SPTYSPTSPS YSPTSPQYSP
1760 1770 1780 1790 1800
TSPQYSPSSP TYTPSSPTYN PTSPRGFSSP QYSPTSPTYS PTSPSYTPSS
1810 1820 1830 1840 1850
PQYSPTSPTY TPSPSEQPGT SAQYSPTSPT YSPSSPTYSP ASPSYSPSSP

TYDPNS
Length:1,856
Mass (Da):204,525
Last modified:March 21, 2012 - v3
Checksum:i379BB183B957D2D5
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti215V → D in AAA28126 (PubMed:2586513).Curated1
Sequence conflicti412 – 415Missing in AAA28126 (PubMed:2586513).Curated4
Sequence conflicti915R → RVSVAQNAIKL in AAA28126 (PubMed:2586513).Curated1
Sequence conflicti963I → D in AAA28126 (PubMed:2586513).Curated1
Sequence conflicti978Q → L in AAA28126 (PubMed:2586513).Curated1
Sequence conflicti994 – 995KP → NA in AAA28126 (PubMed:2586513).Curated2
Sequence conflicti1160 – 1162Missing in AAA28126 (PubMed:2586513).Curated3
Sequence conflicti1406 – 1407IT → YS in AAA28126 (PubMed:2586513).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M29235 mRNA Translation: AAA28126.1
FO081153 Genomic DNA Translation: CCD69532.1
PIRiA34092
T29959
RefSeqiNP_500523.4, NM_068122.6
UniGeneiCel.13014

Genome annotation databases

EnsemblMetazoaiF36A4.7.1; F36A4.7.1; WBGene00000123
F36A4.7.2; F36A4.7.2; WBGene00000123
GeneIDi177190
KEGGicel:CELE_F36A4.7
UCSCiF36A4.7 c. elegans

Similar proteinsi

Entry informationi

Entry nameiRPB1_CAEEL
AccessioniPrimary (citable) accession number: P16356
Secondary accession number(s): Q20090
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: March 21, 2012
Last modified: July 18, 2018
This is version 157 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. SIMILARITY comments
    Index of protein domains and families

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