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Protein

DNA-directed RNA polymerase II subunit rpb1

Gene

polr2a

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript 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).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi66 – 661Zinc 1By similarity
Metal bindingi69 – 691Zinc 1By similarity
Metal bindingi76 – 761Zinc 1By similarity
Metal bindingi79 – 791Zinc 1By similarity
Metal bindingi106 – 1061Zinc 2By similarity
Metal bindingi109 – 1091Zinc 2By similarity
Metal bindingi147 – 1471Zinc 2By similarity
Metal bindingi175 – 1751Zinc 2By similarity
Metal bindingi486 – 4861Magnesium 1; catalyticBy similarity
Metal bindingi486 – 4861Magnesium 2; shared with RPB2By similarity
Metal bindingi488 – 4881Magnesium 1; catalyticBy similarity
Metal bindingi488 – 4881Magnesium 2; shared with RPB2By similarity
Metal bindingi490 – 4901Magnesium 1; catalyticBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-DDI-112382. Formation of RNA Pol II elongation complex.
R-DDI-113418. Formation of the Early Elongation Complex.
R-DDI-674695. RNA Polymerase II Pre-transcription Events.
R-DDI-6781823. Formation of TC-NER Pre-Incision Complex.
R-DDI-6782135. Dual incision in TC-NER.
R-DDI-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-DDI-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-DDI-6807505. RNA polymerase II transcribes snRNA genes.
R-DDI-72086. mRNA Capping.
R-DDI-72165. mRNA Splicing - Minor Pathway.
R-DDI-73776. RNA Polymerase II Promoter Escape.
R-DDI-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-DDI-75953. RNA Polymerase II Transcription Initiation.
R-DDI-75955. RNA Polymerase II Transcription Elongation.
R-DDI-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-DDI-77075. RNA Pol II CTD phosphorylation and interaction with CE.

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 subunit A
Gene namesi
Name:polr2a
Synonyms:rpb1, rpoA
ORF Names:DDB_G0279193
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
Proteomesi
  • UP000002195 Componentsi: Chromosome 3, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0279193. rpb1.

Subcellular locationi

GO - Cellular componenti

  • DNA-directed RNA polymerase II, core complex Source: dictyBase
  • nucleus Source: dictyBase
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 17271727DNA-directed RNA polymerase II subunit rpb1PRO_0000073936Add
BLAST

Post-translational modificationi

The tandem heptapeptide 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. 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

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP35084.
PRIDEiP35084.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.By similarity

Protein-protein interaction databases

STRINGi44689.DDB0215406.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati1553 – 155971
Repeati1560 – 156672
Repeati1567 – 157373
Repeati1574 – 158074
Repeati1581 – 158775
Repeati1588 – 159476
Repeati1595 – 160177
Repeati1602 – 160878
Repeati1609 – 161579
Repeati1616 – 1622710
Repeati1623 – 1629711
Repeati1630 – 1636712
Repeati1637 – 1643713
Repeati1644 – 1650714
Repeati1651 – 1657715
Repeati1658 – 1664716
Repeati1665 – 1671717
Repeati1672 – 1678718
Repeati1679 – 1685719
Repeati1686 – 1692720
Repeati1693 – 1699721
Repeati1700 – 1706722
Repeati1707 – 1713723

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni819 – 83113Bridging helixBy similarityAdd
BLAST
Regioni1553 – 1713161C-terminal domain (CTD); 23 X 7 AA tandem repeats of Y-S-P-[ST]-S-P-[FST]Add
BLAST

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.
InParanoidiP35084.
KOiK03006.
OMAiTGDNSWP.
PhylomeDBiP35084.

Family and domain databases

InterProiIPR000722. 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.
[Graphical view]
PfamiPF04997. 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.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 22 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P35084-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAFFPPSSA ELRKVKRVQF GILSPDEIRN MSVARVEHPE TYENGKPKAG
60 70 80 90 100
GLLDPAMGTI DKTQRCQTCS GTMAECPGHF GHIELAKPVF HIGFIDTVLK
110 120 130 140 150
ILRCVCYHCS KLLTDTNEHS FRQALKIRNQ KHRLNAVVDC CKNKKVCAIG
160 170 180 190 200
GEEEEEHDLS KTDEELDKPV KHGGCGNVLP KITKEDLKII VEFKDVTDES
210 220 230 240 250
IEKKSVLSAE RVLNILKRIK DEDSRAMGIN PDWARADWMI ATVLPVPPPP
260 270 280 290 300
VRPSIMMDTS TRGEDDLTHK LADIVKANRE LQRQEKNGAP AHIIAEATQF
310 320 330 340 350
LQFHVATYVD NEIPGLPQAQ QRSGRPLKSI RQRLKGKEGR IRGNLMGKRV
360 370 380 390 400
DFSARTVITA DPNLSIDQVG VPRSIALNLT YPETVTPFNI DKMRELIRNG
410 420 430 440 450
PSEHPGAKYI IREDGTRFDL RFVKKVSDTH LECGYKVERH INDGDVVIFN
460 470 480 490 500
RQPSLHKMSM MGHRIKVMPY STFRLNLSVT SPYNADFDGD EMNLHVPQTL
510 520 530 540 550
ETRAEVIEIM MVPRQIVSPQ SNRPVMGIVQ DTLLGSRLFT KRDCFMEKDL
560 570 580 590 600
VMNILMWLPS WDGKVPPPAI LKPKQLWTGK QLFSLIIPDI NLIRFTSTHN
610 620 630 640 650
DKEPNECSAG DTRVIIERGE LLAGILCKRS LGAANGSIIH VVMNEHGHDT
660 670 680 690 700
CRLFIDQTQT VVNHWLINRG FTMGIGDTIA DSATMAKVTL TISSAKNQVK
710 720 730 740 750
ELIIKAQNKQ FECQPGKSVI ETFEQKVNQV LNKARDTAGS SAQDSLSEDN
760 770 780 790 800
NLKAMVTAGS KGSFINISQM MACVGQQNVE GKRIPFGFQS RTLPHFTKDD
810 820 830 840 850
YGPESRGFVE NSYLRGLTPQ EFFFHAMGGR EGLIDTAVKT SETGYIQRRL
860 870 880 890 900
VKAMEDVSIK YDATVRNSLG DVIQFAYGED GIDGCFVENQ SIDSLRKDNT
910 920 930 940 950
ELERMYRHQV DKPDYGDGWM DPLVIEHVRN DSLTRDTLEK EFERIKSDRS
960 970 980 990 1000
LLRNEIIPSG EANWPLPVNL RRLINNAQKL FNIDIRRVSD LNPAVVVLEI
1010 1020 1030 1040 1050
EKLVARLKII ATADTTEDDE NFNRAWAEVY FNATMLFSIL VRSTFASKRV
1060 1070 1080 1090 1100
LTEFRLTEKA FLWVCGEIES KFLQALAHPG EMVGALAAQS IGEPATQMTL
1110 1120 1130 1140 1150
NTFHYAGVSS KNVTLGVPRL KEIINIAKQV KTPSLTIYLK PHMARDMDRA
1160 1170 1180 1190 1200
KIVKSQLEYT TLANVTSATE IYYDPDPQNT IISEDAEFVN SYFELPDEEI
1210 1220 1230 1240 1250
DVHSMSPWLL RIELDRGMVT DKKLTMADIT QCVVRDFGLS LNCIFSDDNA
1260 1270 1280 1290 1300
EKLILRIRMV ESQETKGTDN DDDDQFLRRI ESNMLSEMVL RGIKGIKKVF
1310 1320 1330 1340 1350
MRTDDKIPKV TENGGFGVRE EWILDTDGVS LLEVMSHPDV DHTRTTSNDI
1360 1370 1380 1390 1400
VEIIQVLGIE AVRNALLKEL RAVISFDGSY VNYRHLAILA DVMTYRGHLM
1410 1420 1430 1440 1450
AITRHGINRV ETGPLMRCSF EETVEILMDA AMFSETDDVK GVTENIILGQ
1460 1470 1480 1490 1500
LPPLGTGSFE VFLNQDMIKN AHSIALPEPS NVSYPDTPGS QTPSYSYGDG
1510 1520 1530 1540 1550
STTPFHNPYD APLSPFNETF RGDFSPSAMN SPGYNANKSY GSSYQYFPQS
1560 1570 1580 1590 1600
PTYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP
1610 1620 1630 1640 1650
FYSPTSPSYS PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS
1660 1670 1680 1690 1700
YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS PTSPSYSPSS PSYSPSSPSY
1710 1720
SPSSPSYSPS SPTFTNKYNY QPNNKKK
Length:1,727
Mass (Da):192,740
Last modified:December 4, 2007 - v2
Checksum:i6A72F20A508EC68E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti849 – 8491R → C in AAB24966 (PubMed:1482555).Curated
Sequence conflicti1121 – 11222KE → NQ in AAB24966 (PubMed:1482555).Curated
Sequence conflicti1305 – 13051D → E in AAB24966 (PubMed:1482555).Curated
Sequence conflicti1314 – 13141G → S in AAB24966 (PubMed:1482555).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000030 Genomic DNA. Translation: EAL67745.1.
S52651 mRNA. Translation: AAB24966.1.
PIRiA56823.
RefSeqiXP_641735.1. XM_636643.1.

Genome annotation databases

EnsemblProtistsiDDB0215406; DDB0215406; DDB_G0279193.
GeneIDi8621932.
KEGGiddi:DDB_G0279193.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000030 Genomic DNA. Translation: EAL67745.1.
S52651 mRNA. Translation: AAB24966.1.
PIRiA56823.
RefSeqiXP_641735.1. XM_636643.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0215406.

Proteomic databases

PaxDbiP35084.
PRIDEiP35084.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiDDB0215406; DDB0215406; DDB_G0279193.
GeneIDi8621932.
KEGGiddi:DDB_G0279193.

Organism-specific databases

dictyBaseiDDB_G0279193. rpb1.

Phylogenomic databases

eggNOGiKOG0260. Eukaryota.
COG0086. LUCA.
InParanoidiP35084.
KOiK03006.
OMAiTGDNSWP.
PhylomeDBiP35084.

Enzyme and pathway databases

ReactomeiR-DDI-112382. Formation of RNA Pol II elongation complex.
R-DDI-113418. Formation of the Early Elongation Complex.
R-DDI-674695. RNA Polymerase II Pre-transcription Events.
R-DDI-6781823. Formation of TC-NER Pre-Incision Complex.
R-DDI-6782135. Dual incision in TC-NER.
R-DDI-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-DDI-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-DDI-6807505. RNA polymerase II transcribes snRNA genes.
R-DDI-72086. mRNA Capping.
R-DDI-72165. mRNA Splicing - Minor Pathway.
R-DDI-73776. RNA Polymerase II Promoter Escape.
R-DDI-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-DDI-75953. RNA Polymerase II Transcription Initiation.
R-DDI-75955. RNA Polymerase II Transcription Elongation.
R-DDI-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-DDI-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

PROiP35084.

Family and domain databases

InterProiIPR000722. 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.
[Graphical view]
PfamiPF04997. 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.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 22 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome of the social amoeba Dictyostelium discoideum."
    Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
    , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
    Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.
  2. "The largest subunit of RNA polymerase II in Dictyostelium: conservation of the unique tail domain and gene expression."
    Lam T.Y., Chan L., Yip P., Siu C.H.
    Biochem. Cell Biol. 70:792-799(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 826-1727.

Entry informationi

Entry nameiRPB1_DICDI
AccessioniPrimary (citable) accession number: P35084
Secondary accession number(s): Q54X42
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: December 4, 2007
Last modified: June 8, 2016
This is version 103 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.