P38420 (RPB2_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA-directed RNA polymerase II subunit RPB2
Short name=RNA polymerase II subunit 2
Short name=RNA polymerase II subunit B2
EC=2.7.7.6

Alternative name(s):
DNA-directed RNA polymerase II 135 kDa polypeptide
Protein EMBRYO DEFECTIVE 1989

Gene names

Name:	RPB135
Synonyms:	EMB1989, RP140, RPB2
Ordered Locus Names:	At4g21710
ORF Names:	F17L22.170

Organism

Arabidopsis thaliana (Mouse-ear cress)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	1188 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	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. RPB2 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.
Catalytic activity	Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).
Subunit structure	Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits By similarity.
Subcellular location	Nucleus By similarity.
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.
Sequence similarities	Belongs to the RNA polymerase beta chain family.

Ontologies

Keywords
Biological process	Transcription
Cellular component	DNA-directed RNA polymerase Nucleus
Domain	Zinc-finger
Ligand	Magnesium Metal-binding Zinc
Molecular function	Nucleotidyltransferase Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Cellular component	DNA-directed RNA polymerase II, core complex Inferred from physical interaction. Source: TAIR cytosol Inferred from direct assay. Source: TAIR plasmodesma Inferred from direct assay. Source: TAIR
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW ribonucleoside binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1188	1188	DNA-directed RNA polymerase II subunit RPB2		PRO_0000048081
Regions
	Zinc finger	1124 – 1145	22	C4-type
	Compositional bias	14 – 20	7	Asp/Glu-rich (acidic)
Sites
	Metal binding	800	1	Magnesium; shared with RPB1 By similarity
	Metal binding	1124	1	Zinc By similarity
	Metal binding	1127	1	Zinc By similarity
	Metal binding	1142	1	Zinc By similarity
	Metal binding	1145	1	Zinc By similarity
Natural variations
	Natural variant	787	1	I → N.
Experimental info
	Sequence conflict	354 – 355	2	PH → LY in CAA79527. Ref.1
	Sequence conflict	354 – 355	2	PH → LY in CAA79528. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P38420 [UniParc]. Last modified June 20, 2002. Version 2. Checksum: C304E43515C2C364	FASTA	1,188	135,019
	10 20 30 40 50 60 MEYNEYEPEP QYVEDDDDEE ITQEDAWAVI SAYFEEKGLV RQQLDSFDEF IQNTMQEIVD 70 80 90 100 110 120 ESADIEIRPE SQHNPGHQSD FAETIYKISF GQIYLSKPMM TESDGETATL FPKAARLRNL 130 140 150 160 170 180 TYSAPLYVDV TKRVIKKGHD GEEVTETQDF TKVFIGKVPI MLRSSYCTLF QNSEKDLTEL 190 200 210 220 230 240 GECPYDQGGY FIINGSEKVL IAQEKMSTNH VYVFKKRQPN KYAYVGEVRS MAENQNRPPS 250 260 270 280 290 300 TMFVRMLARA SAKGGSSGQY IRCTLPYIRT EIPIIIVFRA LGFVADKDIL EHICYDFADT 310 320 330 340 350 360 QMMELLRPSL EEAFVIQNQL VALDYIGKRG ATVGVTKEKR IKYARDILQK EMLPHVGIGE 370 380 390 400 410 420 HCETKKAYYF GYIIHRLLLC ALGRRPEDDR DHYGNKRLDL AGPLLGGLFR MLFRKLTRDV 430 440 450 460 470 480 RSYVQKCVDN GKEVNLQFAI KAKTITSGLK YSLATGNWGQ ANAAGTRAGV SQVLNRLTYA 490 500 510 520 530 540 STLSHLRRLN SPIGREGKLA KPRQLHNSQW GMMCPAETPE GQACGLVKNL ALMVYITVGS 550 560 570 580 590 600 AAYPILEFLE EWGTENFEEI SPSVIPQATK IFVNGMWVGV HRDPDMLVKT LRRLRRRVDV 610 620 630 640 650 660 NTEVGVVRDI RLKELRIYTD YGRCSRPLFI VDNQKLLIKK RDIYALQQRE SAEEDGWHHL 670 680 690 700 710 720 VAKGFIEYID TEEEETTMIS MTISDLVQAR LRPEEAYTEN YTHCEIHPSL ILGVCASIIP 730 740 750 760 770 780 FPDHNQSPRN TYQSAMGKQA MGIYVTNYQF RMDTLAYVLY YPQKPLVTTR AMEHLHFRQL 790 800 810 820 830 840 PAGINAIVAI SCYSGYNQED SVIMNQSSID RGFFRSLFFR SYRDEEKKMG TLVKEDFGRP 850 860 870 880 890 900 DRGSTMGMRH GSYDKLDDDG LAPPGTRVSG EDVIIGKTTP ISQDEAQGQS SRYTRRDHSI 910 920 930 940 950 960 SLRHSETGMV DQVLLTTNAD GLRFVKVRVR SVRIPQIGDK FSSRHGQKGT VGMTYTQEDM 970 980 990 1000 1010 1020 PWTIEGVTPD IIVNPHAIPS RMTIGQLIEC IMGKVAAHMG KEGDATPFTD VTVDNISKAL 1030 1040 1050 1060 1070 1080 HKCGYQMRGF ERMYNGHTGR PLTAMIFLGP TYYQRLKHMV DDKIHSRGRG PVQILTRQPA 1090 1100 1110 1120 1130 1140 EGRSRDGGLR FGEMERDCMI AHGAAHFLKE RLFDQSDAYR VHVCEVCGLI AIANLKKNSF 1150 1160 1170 1180 ECRGCKNKTD IVQVYIPYAC KLLFQELMSM AIAPRMLTKH LKSAKGRQ

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 8451172] [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: 10617198] [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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00524372.
PIR	T05846.
RefSeq	NP_193902.1. NM_118291.3.
UniGene	At.112.
3D structure databases
ProteinModelPortal	P38420.
ModBase	Search...
Protein-protein interaction databases
STRING	P38420.
Proteomic databases
PRIDE	P38420.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT4G21710.1; AT4G21710.1; AT4G21710.
GeneID	828259.
GenomeReviews	Gene locus AT4G21710 in contig CT486007_GR.
KEGG	ath:AT4G21710.
NMPDR	fig|3702.1.peg.20016.
Organism-specific databases
TAIR	At4g21710.
Phylogenomic databases
eggNOG	KOG0214.
GeneTree	EPGT00070000030528.
HOGENOM	HBG317648.
InParanoid	P38420.
OMA	FGPTYYQ.
PhylomeDB	P38420.
ProtClustDB	CLSN2685591.
Gene expression databases
Genevestigator	P38420.
GermOnline	AT4G21710. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR015712. 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]
Gene3D	G3DSA:2.40.270.10. G3DSA:2.40.270.10. 2 hits. G3DSA:2.40.50.150. Ribosomal_L2. 1 hit.
KO	K03010.
PANTHER	PTHR20856. RNA_pol_I_sub2. 1 hit.
Pfam	PF04563. 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]
PROSITE	PS01166. RNA_POL_BETA. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPB2_ARATH

Accession

Primary (citable) accession number: P38420
Secondary accession number(s): Q9SVS6

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	June 20, 2002
Last modified:	November 16, 2011
This is version 97 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program