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Protein

DNA-directed RNA polymerase II subunit 1

Gene

NRPB1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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. NRPB1 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 NRPB1 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 (NRPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing.1 Publication

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 1; via tele nitrogenBy similarity1
Metal bindingi106Zinc 2By similarity1
Metal bindingi109Zinc 2By similarity1
Metal bindingi147Zinc 2By similarity1
Metal bindingi172Zinc 2By similarity1
Metal bindingi495Magnesium; catalyticBy similarity1
Metal bindingi497Magnesium; catalyticBy similarity1
Metal bindingi499Magnesium; catalyticBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi326 – 397By similarityAdd BLAST72

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-ATH-113418. Formation of the Early Elongation Complex.
R-ATH-674695. RNA Polymerase II Pre-transcription Events.
R-ATH-6781823. Formation of TC-NER Pre-Incision Complex.
R-ATH-6782135. Dual incision in TC-NER.
R-ATH-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-ATH-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-ATH-72086. mRNA Capping.
R-ATH-72163. mRNA Splicing - Major Pathway.
R-ATH-72165. mRNA Splicing - Minor Pathway.
R-ATH-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-ATH-73776. RNA Polymerase II Promoter Escape.
R-ATH-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-ATH-75953. RNA Polymerase II Transcription Initiation.
R-ATH-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-ATH-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit 1
Alternative name(s):
DNA-directed RNA polymerase II subunit RPB1 (EC:2.7.7.6)
Short name:
DNA polymerase II subunit B1
DNA-directed RNA polymerase III largest subunit
Gene namesi
Name:NRPB1
Synonyms:RPB1, RPB205, RPII
Ordered Locus Names:At4g35800
ORF Names:F4B14.70
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G35800.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000739331 – 1839DNA-directed RNA polymerase II subunit 1Add BLAST1839

Post-translational modificationi

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. 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.

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP18616.

PTM databases

iPTMnetiP18616.

Expressioni

Gene expression databases

GenevisibleiP18616. AT.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of at least 12 subunits. Interacts with RDM1. Interacts (via CTD) with MED35A, MED35B, MED35C and CYP59 (PubMed:16497658, PubMed:19110459, PubMed:19467629, PubMed:20410883). Interacts with MEE12/CCG1 and MEE14/CBP1 (PubMed:26462908).5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CYP59Q6Q1513EBI-1540537,EBI-1625989

Protein-protein interaction databases

BioGridi15016. 14 interactors.
DIPiDIP-40008N.
IntActiP18616. 2 interactors.
STRINGi3702.AT4G35800.1.

Structurei

3D structure databases

ProteinModelPortaliP18616.
SMRiP18616.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati1544 – 155017
Repeati1551 – 155727
Repeati1558 – 156437
Repeati1565 – 157147
Repeati1572 – 157857
Repeati1579 – 158567
Repeati1586 – 159277
Repeati1593 – 159987
Repeati1600 – 160697
Repeati1607 – 1613107
Repeati1614 – 1620117
Repeati1621 – 1627127
Repeati1628 – 1634137
Repeati1635 – 1641147
Repeati1642 – 1648157
Repeati1649 – 1655167
Repeati1656 – 1662177
Repeati1663 – 1669187
Repeati1670 – 1676197
Repeati1677 – 1683207
Repeati1684 – 1690217
Repeati1691 – 1697227
Repeati1698 – 1704237
Repeati1705 – 1711247
Repeati1712 – 1718257
Repeati1719 – 1725267
Repeati1726 – 1732277
Repeati1733 – 173828; approximate6
Repeati1739 – 1745297
Repeati1752 – 1758307
Repeati1759 – 1765317
Repeati1766 – 1772327
Repeati1773 – 1779337
Repeati1780 – 1786347
Repeati1794 – 179935; approximate6
Repeati1800 – 1806367
Repeati1807 – 1813377

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni785 – 795Alpha-amanitin bindingAdd BLAST11
Regioni829 – 841Bridging helixAdd BLAST13
Regioni1544 – 1813C-terminal domain (CTD); 37 X 7 AA tandem approximate repeats of Y-[GNS]-P-[QST]-[LNS]-[APT]-[AGKNRSTY]Add BLAST270

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.
HOGENOMiHOG000222975.
InParanoidiP18616.
KOiK03006.
OMAiDEDNGPY.
OrthoDBiEOG09360051.
PhylomeDBiP18616.

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.
PF05001. RNA_pol_Rpb1_R. 15 hits.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 23 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P18616-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDTRFPFSPA EVSKVRVVQF GILSPDEIRQ MSVIHVEHSE TTEKGKPKVG
60 70 80 90 100
GLSDTRLGTI DRKVKCETCM ANMAECPGHF GYLELAKPMY HVGFMKTVLS
110 120 130 140 150
IMRCVCFNCS KILADEEEHK FKQAMKIKNP KNRLKKILDA CKNKTKCDGG
160 170 180 190 200
DDIDDVQSHS TDEPVKKSRG GCGAQQPKLT IEGMKMIAEY KIQRKKNDEP
210 220 230 240 250
DQLPEPAERK QTLGADRVLS VLKRISDADC QLLGFNPKFA RPDWMILEVL
260 270 280 290 300
PIPPPPVRPS VMMDATSRSE DDLTHQLAMI IRHNENLKRQ EKNGAPAHII
310 320 330 340 350
SEFTQLLQFH IATYFDNELP GQPRATQKSG RPIKSICSRL KAKEGRIRGN
360 370 380 390 400
LMGKRVDFSA RTVITPDPTI NIDELGVPWS IALNLTYPET VTPYNIERLK
410 420 430 440 450
ELVDYGPHPP PGKTGAKYII RDDGQRLDLR YLKKSSDQHL ELGYKVERHL
460 470 480 490 500
QDGDFVLFNR QPSLHKMSIM GHRIRIMPYS TFRLNLSVTS PYNADFDGDE
510 520 530 540 550
MNMHVPQSFE TRAEVLELMM VPKCIVSPQA NRPVMGIVQD TLLGCRKITK
560 570 580 590 600
RDTFIEKDVF MNTLMWWEDF DGKVPAPAIL KPRPLWTGKQ VFNLIIPKQI
610 620 630 640 650
NLLRYSAWHA DTETGFITPG DTQVRIERGE LLAGTLCKKT LGTSNGSLVH
660 670 680 690 700
VIWEEVGPDA ARKFLGHTQW LVNYWLLQNG FTIGIGDTIA DSSTMEKINE
710 720 730 740 750
TISNAKTAVK DLIRQFQGKE LDPEPGRTMR DTFENRVNQV LNKARDDAGS
760 770 780 790 800
SAQKSLAETN NLKAMVTAGS KGSFINISQM TACVGQQNVE GKRIPFGFDG
810 820 830 840 850
RTLPHFTKDD YGPESRGFVE NSYLRGLTPQ EFFFHAMGGR EGLIDTAVKT
860 870 880 890 900
SETGYIQRRL VKAMEDIMVK YDGTVRNSLG DVIQFLYGED GMDAVWIESQ
910 920 930 940 950
KLDSLKMKKS EFDRTFKYEI DDENWNPTYL SDEHLEDLKG IRELRDVFDA
960 970 980 990 1000
EYSKLETDRF QLGTEIATNG DSTWPLPVNI KRHIWNAQKT FKIDLRKISD
1010 1020 1030 1040 1050
MHPVEIVDAV DKLQERLLVV PGDDALSVEA QKNATLFFNI LLRSTLASKR
1060 1070 1080 1090 1100
VLEEYKLSRE AFEWVIGEIE SRFLQSLVAP GEMIGCVAAQ SIGEPATQMT
1110 1120 1130 1140 1150
LNTFHYAGVS AKNVTLGVPR LREIINVAKR IKTPSLSVYL TPEASKSKEG
1160 1170 1180 1190 1200
AKTVQCALEY TTLRSVTQAT EVWYDPDPMS TIIEEDFEFV RSYYEMPDED
1210 1220 1230 1240 1250
VSPDKISPWL LRIELNREMM VDKKLSMADI AEKINLEFDD DLTCIFNDDN
1260 1270 1280 1290 1300
AQKLILRIRI MNDEGPKGEL QDESAEDDVF LKKIESNMLT EMALRGIPDI
1310 1320 1330 1340 1350
NKVFIKQVRK SRFDEEGGFK TSEEWMLDTE GVNLLAVMCH EDVDPKRTTS
1360 1370 1380 1390 1400
NHLIEIIEVL GIEAVRRALL DELRVVISFD GSYVNYRHLA ILCDTMTYRG
1410 1420 1430 1440 1450
HLMAITRHGI NRNDTGPLMR CSFEETVDIL LDAAAYAETD CLRGVTENIM
1460 1470 1480 1490 1500
LGQLAPIGTG DCELYLNDEM LKNAIELQLP SYMDGLEFGM TPARSPVSGT
1510 1520 1530 1540 1550
PYHEGMMSPN YLLSPNMRLS PMSDAQFSPY VGGMAFSPSS SPGYSPSSPG
1560 1570 1580 1590 1600
YSPTSPGYSP TSPGYSPTSP GYSPTSPTYS PSSPGYSPTS PAYSPTSPSY
1610 1620 1630 1640 1650
SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP AYSPTSPAYS
1660 1670 1680 1690 1700
PTSPAYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPAYSP
1710 1720 1730 1740 1750
TSPGYSPTSP SYSPTSPSYG PTSPSYNPQS AKYSPSIAYS PSNARLSPAS
1760 1770 1780 1790 1800
PYSPTSPNYS PTSPSYSPTS PSYSPSSPTY SPSSPYSSGA SPDYSPSAGY
1810 1820 1830
SPTLPGYSPS STGQYTPHEG DKKDKTGKKD ASKDDKGNP
Length:1,839
Mass (Da):204,626
Last modified:February 8, 2011 - v3
Checksum:i7B8488DBB5180B40
GO

Sequence cautioni

The sequence CAA36735 differs from that shown. Reason: Erroneous gene model prediction.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti117 – 122EEHKFK → VCRSLFR in CAA37130 (PubMed:2259344).Curated6
Sequence conflicti192 – 196IQRKK → NSKEE in CAA36735 (PubMed:2103447).Curated5
Sequence conflicti297A → R in CAA36735 (PubMed:2103447).Curated1
Sequence conflicti302E → R in CAA36735 (PubMed:2103447).Curated1
Sequence conflicti400 – 416KELVD…GKTGA → VRLVFISFSET in CAA37130 (PubMed:2259344).CuratedAdd BLAST17
Sequence conflicti427L → S in CAA37130 (PubMed:2259344).Curated1
Sequence conflicti738N → D in CAA37130 (PubMed:2259344).Curated1
Sequence conflicti1061A → R in CAA37130 (PubMed:2259344).Curated1
Sequence conflicti1088A → P in CAA36735 (PubMed:2103447).Curated1
Sequence conflicti1719Y → YSPTSPSY in CAA37130 (PubMed:2259344).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X52954 Genomic DNA. Translation: CAA37130.1.
X52494 Genomic DNA. Translation: CAA36735.1. Sequence problems.
AL031986 Genomic DNA. Translation: CAA21466.2.
AL161588 Genomic DNA. Translation: CAB81489.1.
CP002687 Genomic DNA. Translation: AEE86573.1.
AK221166 mRNA. Translation: BAD95215.1.
PIRiG85422.
T04690. JDMU1.
RefSeqiNP_195305.2. NM_119746.4.
UniGeneiAt.23499.
At.67132.

Genome annotation databases

EnsemblPlantsiAT4G35800.1; AT4G35800.1; AT4G35800.
GeneIDi829734.
GrameneiAT4G35800.1; AT4G35800.1; AT4G35800.
KEGGiath:AT4G35800.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X52954 Genomic DNA. Translation: CAA37130.1.
X52494 Genomic DNA. Translation: CAA36735.1. Sequence problems.
AL031986 Genomic DNA. Translation: CAA21466.2.
AL161588 Genomic DNA. Translation: CAB81489.1.
CP002687 Genomic DNA. Translation: AEE86573.1.
AK221166 mRNA. Translation: BAD95215.1.
PIRiG85422.
T04690. JDMU1.
RefSeqiNP_195305.2. NM_119746.4.
UniGeneiAt.23499.
At.67132.

3D structure databases

ProteinModelPortaliP18616.
SMRiP18616.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi15016. 14 interactors.
DIPiDIP-40008N.
IntActiP18616. 2 interactors.
STRINGi3702.AT4G35800.1.

PTM databases

iPTMnetiP18616.

Proteomic databases

PaxDbiP18616.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G35800.1; AT4G35800.1; AT4G35800.
GeneIDi829734.
GrameneiAT4G35800.1; AT4G35800.1; AT4G35800.
KEGGiath:AT4G35800.

Organism-specific databases

TAIRiAT4G35800.

Phylogenomic databases

eggNOGiKOG0260. Eukaryota.
COG0086. LUCA.
HOGENOMiHOG000222975.
InParanoidiP18616.
KOiK03006.
OMAiDEDNGPY.
OrthoDBiEOG09360051.
PhylomeDBiP18616.

Enzyme and pathway databases

ReactomeiR-ATH-113418. Formation of the Early Elongation Complex.
R-ATH-674695. RNA Polymerase II Pre-transcription Events.
R-ATH-6781823. Formation of TC-NER Pre-Incision Complex.
R-ATH-6782135. Dual incision in TC-NER.
R-ATH-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-ATH-6796648. TP53 Regulates Transcription of DNA Repair Genes.
R-ATH-72086. mRNA Capping.
R-ATH-72163. mRNA Splicing - Major Pathway.
R-ATH-72165. mRNA Splicing - Minor Pathway.
R-ATH-72203. Processing of Capped Intron-Containing Pre-mRNA.
R-ATH-73776. RNA Polymerase II Promoter Escape.
R-ATH-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-ATH-75953. RNA Polymerase II Transcription Initiation.
R-ATH-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-ATH-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

PROiP18616.

Gene expression databases

GenevisibleiP18616. AT.

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.
PF05001. RNA_pol_Rpb1_R. 15 hits.
[Graphical view]
SMARTiSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEiPS00115. RNA_POL_II_REPEAT. 23 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNRPB1_ARATH
AccessioniPrimary (citable) accession number: P18616
Secondary accession number(s): P31635, Q56Z04, Q9SZS8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: February 8, 2011
Last modified: November 30, 2016
This is version 157 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  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.