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Reviewed, UniProtKB/Swiss-Prot P18616 (RPB1_ARATH)

Last modified November 3, 2009. Version 95. Feed History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    DNA-directed RNA polymerase II subunit RPB1
      Short name=RNA polymerase II subunit B1
    EC=2.7.7.6
Alternative name(s):
    DNA-directed RNA polymerase III largest subunit
Gene names
Name: RPB205
Synonyms: RPB1, RPII
Ordered Locus Names: At4g35800
ORF Names: F4B14.70
OrganismArabidopsis thaliana (Mouse-ear cress) [Complete proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

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Protein attributes

Sequence length1840 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
Protein existenceEvidence at protein level.

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General annotation (Comments)

Function

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.

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.

Post-translational modification

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 heptapepdtide repeat. The phosphorylation state is believed to result from the balanced action of site-specific CTD kinases and phosphataes, and a "CTD code" that specifies the position of Pol II within the transcription cycle has been proposed.

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 nucelotide 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.

Sequence similarities

Belongs to the RNA polymerase beta' chain family.

Contains 1 C2H2-type zinc finger.

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Binary interactions

With

Entry

#Exp.

IntAct

Notes

CYP59Q6Q1512EBI-1540537,EBI-1625989

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 18401840DNA-directed RNA polymerase II subunit RPB1
PRO_0000073933

Regions

Repeat1545 – 155171
Repeat1552 – 155872
Repeat1559 – 156573
Repeat1566 – 157274
Repeat1573 – 157975
Repeat1580 – 158676
Repeat1587 – 159377
Repeat1594 – 160078
Repeat1601 – 160779
Repeat1608 – 1614710
Repeat1615 – 1621711
Repeat1622 – 1628712
Repeat1629 – 1635713
Repeat1636 – 1642714
Repeat1643 – 1649715
Repeat1650 – 1656716
Repeat1657 – 1663717
Repeat1664 – 1670718
Repeat1671 – 1677719
Repeat1678 – 1684720
Repeat1685 – 1691721
Repeat1692 – 1698722
Repeat1699 – 1705723
Repeat1706 – 1712724
Repeat1713 – 1719725
Repeat1720 – 1726726
Repeat1727 – 1733727
Repeat1734 – 1739628; approximate
Repeat1740 – 1746729
Repeat1753 – 1759730
Repeat1760 – 1766731
Repeat1767 – 1773732
Repeat1774 – 1780733
Repeat1781 – 1787734
Repeat1795 – 1800635; approximate
Repeat1801 – 1807736
Repeat1808 – 1814737
Zinc finger66 – 7914C2H2-type By similarity
DNA binding327 – 39872 By similarity
Region786 – 79611Alpha-amanitin binding
Region830 – 84213Bridging helix
Region1545 – 181427037 X 7 AA tandem approximate repeats of Y-[GNS]-P-[QST]-[LNS]-[APT]-[AGKNRSTY]

Sites

Metal binding661Zinc 1 By similarity
Metal binding691Zinc 1 By similarity
Metal binding761Zinc 1 By similarity
Metal binding791Zinc 1 By similarity
Metal binding1061Zinc 2 By similarity
Metal binding1091Zinc 2 By similarity
Metal binding1481Zinc 2 By similarity
Metal binding1731Zinc 2 By similarity
Metal binding4961Magnesium 1; catalytic By similarity
Metal binding4961Magnesium 2; shared with RPB2 By similarity
Metal binding4981Magnesium 1; catalytic By similarity
Metal binding4981Magnesium 2; shared with RPB2 By similarity
Metal binding5001Magnesium 1; catalytic By similarity

Experimental info

Sequence conflict117 – 1248Missing in CAA36735. Ref.2
Sequence conflict193 – 1975IQRKK → NSKEE in CAA36735. Ref.2
Sequence conflict2981A → R in CAA36735. Ref.2
Sequence conflict3031E → R in CAA36735. Ref.2
Sequence conflict401 – 41717KELVD…GKTGA → VRLVFISFSET Ref.1
Sequence conflict4281L → S in CAA37130. Ref.1
Sequence conflict4461K → RYVLLSYSIHSTHKRLFLEV VIFMLSWSQ in CAA36735. Ref.2
Sequence conflict7391N → D in CAA37130. Ref.1
Sequence conflict10621A → R in CAA37130. Ref.1
Sequence conflict10891A → P in CAA36735. Ref.2
Sequence conflict17201Y → YSPTSPSY Ref.1

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Sequences

Sequence LengthMass (Da)Tools
P18616-1 [UniParc].

Last modified December 1, 2000. Version 2.
Checksum: 8453621AD945C1B6

FASTA1,840204,690
        10         20         30         40         50         60 
MDTRFPFSPA EVSKVRVVQF GILSPDEIRQ MSVIHVEHSE TTEKGKPKVG GLSDTRLGTI 

        70         80         90        100        110        120 
DRKVKCETCM ANMAECPGHF GYLELAKPMY HVGFMKTVLS IMRCVCFNCS KILADEVCRS 

       130        140        150        160        170        180 
LFRQAMKIKN PKNRLKKILD ACKNKTKCDG GDDIDDVQSH STDEPVKKSR GGCGAQQPKL 

       190        200        210        220        230        240 
TIEGMKMIAE YKIQRKKNDE PDQLPEPAER KQTLGADRVL SVLKRISDAD CQLLGFNPKF 

       250        260        270        280        290        300 
ARPDWMILEV LPIPPPPVRP SVMMDATSRS EDDLTHQLAM IIRHNENLKR QEKNGAPAHI 

       310        320        330        340        350        360 
ISEFTQLLQF HIATYFDNEL PGQPRATQKS GRPIKSICSR LKAKEGRIRG NLMGKRVDFS 

       370        380        390        400        410        420 
ARTVITPDPT INIDELGVPW SIALNLTYPE TVTPYNIERL KELVDYGPHP PPGKTGAKYI 

       430        440        450        460        470        480 
IRDDGQRLDL RYLKKSSDQH LELGYKVERH LQDGDFVLFN RQPSLHKMSI MGHRIRIMPY 

       490        500        510        520        530        540 
STFRLNLSVT SPYNADFDGD EMNMHVPQSF ETRAEVLELM MVPKCIVSPQ ANRPVMGIVQ 

       550        560        570        580        590        600 
DTLLGCRKIT KRDTFIEKDV FMNTLMWWED FDGKVPAPAI LKPRPLWTGK QVFNLIIPKQ 

       610        620        630        640        650        660 
INLLRYSAWH ADTETGFITP GDTQVRIERG ELLAGTLCKK TLGTSNGSLV HVIWEEVGPD 

       670        680        690        700        710        720 
AARKFLGHTQ WLVNYWLLQN GFTIGIGDTI ADSSTMEKIN ETISNAKTAV KDLIRQFQGK 

       730        740        750        760        770        780 
ELDPEPGRTM RDTFENRVNQ VLNKARDDAG SSAQKSLAET NNLKAMVTAG SKGSFINISQ 

       790        800        810        820        830        840 
MTACVGQQNV EGKRIPFGFD GRTLPHFTKD DYGPESRGFV ENSYLRGLTP QEFFFHAMGG 

       850        860        870        880        890        900 
REGLIDTAVK TSETGYIQRR LVKAMEDIMV KYDGTVRNSL GDVIQFLYGE DGMDAVWIES 

       910        920        930        940        950        960 
QKLDSLKMKK SEFDRTFKYE IDDENWNPTY LSDEHLEDLK GIRELRDVFD AEYSKLETDR 

       970        980        990       1000       1010       1020 
FQLGTEIATN GDSTWPLPVN IKRHIWNAQK TFKIDLRKIS DMHPVEIVDA VDKLQERLLV 

      1030       1040       1050       1060       1070       1080 
VPGDDALSVE AQKNATLFFN ILLRSTLASK RVLEEYKLSR EAFEWVIGEI ESRFLQSLVA 

      1090       1100       1110       1120       1130       1140 
PGEMIGCVAA QSIGEPATQM TLNTFHYAGV SAKNVTLGVP RLREIINVAK RIKTPSLSVY 

      1150       1160       1170       1180       1190       1200 
LTPEASKSKE GAKTVQCALE YTTLRSVTQA TEVWYDPDPM STIIEEDFEF VRSYYEMPDE 

      1210       1220       1230       1240       1250       1260 
DVSPDKISPW LLRIELNREM MVDKKLSMAD IAEKINLEFD DDLTCIFNDD NAQKLILRIR 

      1270       1280       1290       1300       1310       1320 
IMNDEGPKGE LQDESAEDDV FLKKIESNML TEMALRGIPD INKVFIKQVR KSRFDEEGGF 

      1330       1340       1350       1360       1370       1380 
KTSEEWMLDT EGVNLLAVMC HEDVDPKRTT SNHLIEIIEV LGIEAVRRAL LDELRVVISF 

      1390       1400       1410       1420       1430       1440 
DGSYVNYRHL AILCDTMTYR GHLMAITRHG INRNDTGPLM RCSFEETVDI LLDAAAYAET 

      1450       1460       1470       1480       1490       1500 
DCLRGVTENI MLGQLAPIGT GDCELYLNDE MLKNAIELQL PSYMDGLEFG MTPARSPVSG 

      1510       1520       1530       1540       1550       1560 
TPYHEGMMSP NYLLSPNMRL SPMSDAQFSP YVGGMAFSPS SSPGYSPSSP GYSPTSPGYS 

      1570       1580       1590       1600       1610       1620 
PTSPGYSPTS PGYSPTSPTY SPSSPGYSPT SPAYSPTSPS YSPTSPSYSP TSPSYSPTSP 

      1630       1640       1650       1660       1670       1680 
SYSPTSPSYS PTSPSYSPTS PAYSPTSPAY SPTSPAYSPT SPSYSPTSPS YSPTSPSYSP 

      1690       1700       1710       1720       1730       1740 
TSPSYSPTSP SYSPTSPAYS PTSPGYSPTS PSYSPTSPSY GPTSPSYNPQ SAKYSPSIAY 

      1750       1760       1770       1780       1790       1800 
SPSNARLSPA SPYSPTSPNY SPTSPSYSPT SPSYSPSSPT YSPSSPYSSG ASPDYSPSAG 

      1810       1820       1830       1840 
YSPTLPGYSP SSTGQYTPHE GDKKDKTGKK DASKDDKGNP

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References

« Hide 'large scale' references
[1]"Homologous domains of the largest subunit of eucaryotic RNA polymerase II are conserved in plants."
Nawrath C., Schell J., Koncz C.
Mol. Gen. Genet. 223:65-75(1990) [PubMed: 2259344] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: cv. Columbia.
[2]"Analysis of the genes encoding the largest subunit of RNA polymerase II in Arabidopsis and soybean."
Dietrich M.A., Prenger J.P., Guilfoyle T.J.
Plant Mol. Biol. 15:207-223(1990) [PubMed: 2103447] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: cv. Columbia.
[3]"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. expand/collapse author list , 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.
+Additional computationally mapped references.

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Cross-references

Sequence databases

X52954 Genomic DNA. Translation: CAA37130.1.
X52494 Genomic DNA. Translation: CAA36735.1.
AL031986 Genomic DNA. Translation: CAA21466.2.
AL161588 Genomic DNA. Translation: CAB81489.1.
IPIIPI00545790.
PIRG85422.
JDMU1. T04690.
RefSeqNP_195305.1.
UniGeneAt.23499
At.67132

3D structure databases

HSSPHSSP built from PDB template 1K83 based on UniProtKB P04050.
ModBaseSearch...

Protein-protein interaction databases

IntActP18616. 1 interaction.
STRINGP18616.

Proteomic databases

PRIDEP18616.

Genome annotation databases

GeneID829734.
GenomeReviewsGene locus AT4G35800 in contig CT486007_GR.
KEGGath:AT4G35800.
NMPDRfig|3702.1.peg.21671.

Organism-specific databases

TAIRAt4g35800.

Phylogenomic databases

OMATSPHYSP.

Enzyme and pathway databases

BRENDA2.7.7.6. 302.

Gene expression databases

ArrayExpressP18616.
GenevestigatorP18616.
GermOnlineAT4G35800. Arabidopsis thaliana.

Family and domain databases

InterProIPR000722. 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]
Gene3DG3DSA:2.40.40.30. RNA_pol_A. 1 hit.
G3DSA:3.90.1120.10. RNA_pol_Rpb1_1. 1 hit.
G3DSA:3.30.1360.90. RNA_pol_Rpb1_7. 1 hit.
PfamPF04997. 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. 18 hits.
[Graphical view]
SMARTSM00663. RPOLA_N. 1 hit.
[Graphical view]
PROSITEPS00115. RNA_POL_II_REPEAT. 23 hits.
[Graphical view]
ProtoNetSearch...

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Entry information

Entry nameRPB1_ARATH
AccessionPrimary (citable) accession number: P18616
Secondary accession number(s): P31635, Q9SZS8
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: December 1, 2000
Last modified: November 3, 2009
This is version 95 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectPPAP (Plant Proteome Annotation Project)

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Relevant documents

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents