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Protein

DNA-directed RNA polymerase II subunit 2

Gene

NRPB2

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. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the 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. NRPB2 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 (By similarity).By similarity
Essential for the completion of the three rounds of mitosis in female megaspores required for the development of mature gametophytes (PubMed:18723889).1 Publication

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi800 – 8001Magnesium; shared with RPB1By similarity
Metal bindingi1124 – 11241ZincBy similarity
Metal bindingi1127 – 11271ZincBy similarity
Metal bindingi1142 – 11421ZincBy similarity
Metal bindingi1145 – 11451ZincBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1124 – 114522C4-typeAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: InterPro
  • DNA-directed RNA polymerase activity Source: TAIR
  • metal ion binding Source: UniProtKB-KW
  • ribonucleoside binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciARA:AT4G21710-MONOMER.
ReactomeiR-ATH-112382. Formation of RNA Pol II elongation complex.
R-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 2
Alternative name(s):
DNA-directed RNA polymerase II 135 kDa polypeptide
DNA-directed RNA polymerase II subunit RPB2 (EC:2.7.7.6)
Short name:
RNA polymerase II subunit 2
Short name:
RNA polymerase II subunit B2
Protein EMBRYO DEFECTIVE 1989
Gene namesi
Name:NRPB2
Synonyms:EMB1989, RP140, RPB135, RPB2
Ordered Locus Names:At4g21710
ORF Names:F17L22.170
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G21710.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

Pathology & Biotechi

Disruption phenotypei

Defect in seed production due to female gametophyte developmental arrest.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11881188DNA-directed RNA polymerase II subunit 2PRO_0000048081Add
BLAST

Proteomic databases

PaxDbiP38420.
PRIDEiP38420.

PTM databases

iPTMnetiP38420.

Expressioni

Gene expression databases

GenevisibleiP38420. AT.

Interactioni

Subunit structurei

Component of the RNA polymerase II complex consisting of at least 12 subunits.1 Publication

Protein-protein interaction databases

BioGridi13548. 4 interactions.
STRINGi3702.AT4G21710.1.

Structurei

3D structure databases

ProteinModelPortaliP38420.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi14 – 207Asp/Glu-rich (acidic)

Sequence similaritiesi

Belongs to the RNA polymerase beta chain family.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1124 – 114522C4-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0214. Eukaryota.
COG0085. LUCA.
HOGENOMiHOG000218612.
InParanoidiP38420.
KOiK03010.
OMAiRTQPHFE.
PhylomeDBiP38420.

Family and domain databases

Gene3Di2.40.270.10. 2 hits.
2.40.50.150. 1 hit.
3.90.1110.10. 1 hit.
InterProiIPR015712. DNA-dir_RNA_pol_su2.
IPR007120. DNA-dir_RNA_pol_su2_6.
IPR007121. RNA_pol_bsu_CS.
IPR007644. RNA_pol_bsu_protrusion.
IPR007642. RNA_pol_Rpb2_2.
IPR007645. RNA_pol_Rpb2_3.
IPR007646. RNA_pol_Rpb2_4.
IPR007647. RNA_pol_Rpb2_5.
IPR007641. RNA_pol_Rpb2_7.
IPR014724. RNA_pol_RPB2_OB-fold.
[Graphical view]
PANTHERiPTHR20856. PTHR20856. 1 hit.
PfamiPF04563. RNA_pol_Rpb2_1. 1 hit.
PF04561. RNA_pol_Rpb2_2. 1 hit.
PF04565. RNA_pol_Rpb2_3. 1 hit.
PF04566. RNA_pol_Rpb2_4. 1 hit.
PF04567. RNA_pol_Rpb2_5. 1 hit.
PF00562. RNA_pol_Rpb2_6. 1 hit.
PF04560. RNA_pol_Rpb2_7. 1 hit.
[Graphical view]
PROSITEiPS01166. RNA_POL_BETA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P38420-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEYNEYEPEP QYVEDDDDEE ITQEDAWAVI SAYFEEKGLV RQQLDSFDEF
60 70 80 90 100
IQNTMQEIVD ESADIEIRPE SQHNPGHQSD FAETIYKISF GQIYLSKPMM
110 120 130 140 150
TESDGETATL FPKAARLRNL TYSAPLYVDV TKRVIKKGHD GEEVTETQDF
160 170 180 190 200
TKVFIGKVPI MLRSSYCTLF QNSEKDLTEL GECPYDQGGY FIINGSEKVL
210 220 230 240 250
IAQEKMSTNH VYVFKKRQPN KYAYVGEVRS MAENQNRPPS TMFVRMLARA
260 270 280 290 300
SAKGGSSGQY IRCTLPYIRT EIPIIIVFRA LGFVADKDIL EHICYDFADT
310 320 330 340 350
QMMELLRPSL EEAFVIQNQL VALDYIGKRG ATVGVTKEKR IKYARDILQK
360 370 380 390 400
EMLPHVGIGE HCETKKAYYF GYIIHRLLLC ALGRRPEDDR DHYGNKRLDL
410 420 430 440 450
AGPLLGGLFR MLFRKLTRDV RSYVQKCVDN GKEVNLQFAI KAKTITSGLK
460 470 480 490 500
YSLATGNWGQ ANAAGTRAGV SQVLNRLTYA STLSHLRRLN SPIGREGKLA
510 520 530 540 550
KPRQLHNSQW GMMCPAETPE GQACGLVKNL ALMVYITVGS AAYPILEFLE
560 570 580 590 600
EWGTENFEEI SPSVIPQATK IFVNGMWVGV HRDPDMLVKT LRRLRRRVDV
610 620 630 640 650
NTEVGVVRDI RLKELRIYTD YGRCSRPLFI VDNQKLLIKK RDIYALQQRE
660 670 680 690 700
SAEEDGWHHL VAKGFIEYID TEEEETTMIS MTISDLVQAR LRPEEAYTEN
710 720 730 740 750
YTHCEIHPSL ILGVCASIIP FPDHNQSPRN TYQSAMGKQA MGIYVTNYQF
760 770 780 790 800
RMDTLAYVLY YPQKPLVTTR AMEHLHFRQL PAGINAIVAI SCYSGYNQED
810 820 830 840 850
SVIMNQSSID RGFFRSLFFR SYRDEEKKMG TLVKEDFGRP DRGSTMGMRH
860 870 880 890 900
GSYDKLDDDG LAPPGTRVSG EDVIIGKTTP ISQDEAQGQS SRYTRRDHSI
910 920 930 940 950
SLRHSETGMV DQVLLTTNAD GLRFVKVRVR SVRIPQIGDK FSSRHGQKGT
960 970 980 990 1000
VGMTYTQEDM PWTIEGVTPD IIVNPHAIPS RMTIGQLIEC IMGKVAAHMG
1010 1020 1030 1040 1050
KEGDATPFTD VTVDNISKAL HKCGYQMRGF ERMYNGHTGR PLTAMIFLGP
1060 1070 1080 1090 1100
TYYQRLKHMV DDKIHSRGRG PVQILTRQPA EGRSRDGGLR FGEMERDCMI
1110 1120 1130 1140 1150
AHGAAHFLKE RLFDQSDAYR VHVCEVCGLI AIANLKKNSF ECRGCKNKTD
1160 1170 1180
IVQVYIPYAC KLLFQELMSM AIAPRMLTKH LKSAKGRQ
Length:1,188
Mass (Da):135,019
Last modified:June 20, 2002 - v2
Checksum:iC304E43515C2C364
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti354 – 3552PH → LY in CAA79527 (PubMed:8451172).Curated
Sequence conflicti354 – 3552PH → LY in CAA79528 (PubMed:8451172).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti787 – 7871I → N.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z19120 mRNA. Translation: CAA79527.1.
Z19121 Genomic DNA. Translation: CAA79528.1.
AL035527 Genomic DNA. Translation: CAB36815.1.
AL161555 Genomic DNA. Translation: CAB81278.1.
CP002687 Genomic DNA. Translation: AEE84493.1.
PIRiT05846.
RefSeqiNP_193902.1. NM_118291.3.
UniGeneiAt.112.

Genome annotation databases

EnsemblPlantsiAT4G21710.1; AT4G21710.1; AT4G21710.
GeneIDi828259.
GrameneiAT4G21710.1; AT4G21710.1; AT4G21710.
KEGGiath:AT4G21710.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z19120 mRNA. Translation: CAA79527.1.
Z19121 Genomic DNA. Translation: CAA79528.1.
AL035527 Genomic DNA. Translation: CAB36815.1.
AL161555 Genomic DNA. Translation: CAB81278.1.
CP002687 Genomic DNA. Translation: AEE84493.1.
PIRiT05846.
RefSeqiNP_193902.1. NM_118291.3.
UniGeneiAt.112.

3D structure databases

ProteinModelPortaliP38420.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi13548. 4 interactions.
STRINGi3702.AT4G21710.1.

PTM databases

iPTMnetiP38420.

Proteomic databases

PaxDbiP38420.
PRIDEiP38420.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G21710.1; AT4G21710.1; AT4G21710.
GeneIDi828259.
GrameneiAT4G21710.1; AT4G21710.1; AT4G21710.
KEGGiath:AT4G21710.

Organism-specific databases

TAIRiAT4G21710.

Phylogenomic databases

eggNOGiKOG0214. Eukaryota.
COG0085. LUCA.
HOGENOMiHOG000218612.
InParanoidiP38420.
KOiK03010.
OMAiRTQPHFE.
PhylomeDBiP38420.

Enzyme and pathway databases

BioCyciARA:AT4G21710-MONOMER.
ReactomeiR-ATH-112382. Formation of RNA Pol II elongation complex.
R-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

PROiP38420.

Gene expression databases

GenevisibleiP38420. AT.

Family and domain databases

Gene3Di2.40.270.10. 2 hits.
2.40.50.150. 1 hit.
3.90.1110.10. 1 hit.
InterProiIPR015712. DNA-dir_RNA_pol_su2.
IPR007120. DNA-dir_RNA_pol_su2_6.
IPR007121. RNA_pol_bsu_CS.
IPR007644. RNA_pol_bsu_protrusion.
IPR007642. RNA_pol_Rpb2_2.
IPR007645. RNA_pol_Rpb2_3.
IPR007646. RNA_pol_Rpb2_4.
IPR007647. RNA_pol_Rpb2_5.
IPR007641. RNA_pol_Rpb2_7.
IPR014724. RNA_pol_RPB2_OB-fold.
[Graphical view]
PANTHERiPTHR20856. PTHR20856. 1 hit.
PfamiPF04563. RNA_pol_Rpb2_1. 1 hit.
PF04561. RNA_pol_Rpb2_2. 1 hit.
PF04565. RNA_pol_Rpb2_3. 1 hit.
PF04566. RNA_pol_Rpb2_4. 1 hit.
PF04567. RNA_pol_Rpb2_5. 1 hit.
PF00562. RNA_pol_Rpb2_6. 1 hit.
PF04560. RNA_pol_Rpb2_7. 1 hit.
[Graphical view]
PROSITEiPS01166. RNA_POL_BETA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The second largest subunit of RNA polymerase II from Arabidopsis thaliana."
    Larkin R., Guilfoyle T.J.
    Nucleic Acids Res. 21:1038-1038(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. Columbia.
  2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Sex-biased lethality or transmission of defective transcription machinery in Arabidopsis."
    Onodera Y., Nakagawa K., Haag J.R., Pikaard D., Mikami T., Ream T., Ito Y., Pikaard C.S.
    Genetics 180:207-218(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
  5. "Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II."
    Ream T.S., Haag J.R., Wierzbicki A.T., Nicora C.D., Norbeck A.D., Zhu J.K., Hagen G., Guilfoyle T.J., Pasa-Tolic L., Pikaard C.S.
    Mol. Cell 33:192-203(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, NOMENCLATURE.

Entry informationi

Entry nameiNRPB2_ARATH
AccessioniPrimary (citable) accession number: P38420
Secondary accession number(s): Q9SVS6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: June 20, 2002
Last modified: July 6, 2016
This is version 132 of the entry and version 2 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 coordinated by three conserved aspartate residues of the two largest RNA Pol II subunits (By similarity).By similarity

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.