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Protein

DNA-directed RNA polymerase II subunit rpb2

Gene

polr2b

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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. 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).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi788 – 7881Magnesium; shared with RPB1By similarity
Metal bindingi1114 – 11141ZincBy similarity
Metal bindingi1117 – 11171ZincBy similarity
Metal bindingi1132 – 11321ZincBy similarity
Metal bindingi1135 – 11351ZincBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1114 – 113522C4-typeAdd
BLAST

GO - Molecular functioni

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

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 rpb2 (EC:2.7.7.6)
Short name:
RNA polymerase II subunit 2
Short name:
RNA polymerase II subunit B2
Gene namesi
Name:polr2b
Synonyms:rpb2
ORF Names:DDB_G0288257
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
Proteomesi
  • UP000002195 Componentsi: Chromosome 5, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0288257. rpb2.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11701170DNA-directed RNA polymerase II subunit rpb2PRO_0000328242Add
BLAST

Proteomic databases

PaxDbiQ54J75.
PRIDEiQ54J75.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi44689.DDB0216277.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi663 – 6664Poly-Glu

Sequence similaritiesi

Belongs to the RNA polymerase beta chain family.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1114 – 113522C4-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0214. Eukaryota.
COG0085. LUCA.
InParanoidiQ54J75.
KOiK03010.
OMAiRTQPHFE.
PhylomeDBiQ54J75.

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.

Q54J75-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDYMMNDDS QDNPHADISQ EDVWTVISAY FQEKGLVRQQ LDSFDEFIQN
60 70 80 90 100
TMQEIIDESP PITLRPESQH HPGQAVVSNN VSTFSVKFGQ IYLSKPTAEI
110 120 130 140 150
DGVSQQVTPN QARIRNLTYS APLFVDITKT VMTGSKSKGD ERRTDEVLKR
160 170 180 190 200
IFIGKVPIML RSQYCMLNEA DDRDLTTMGE CSFDQGGYFI INGSEKVLIA
210 220 230 240 250
QEKMNNNHVY VFKKSPPSKY SYVAEIRSCQ ETGSRPTSTM YLKMLHNTNK
260 270 280 290 300
GPVGIKATVP YIKQDVPVII VFRALGFVAD KDILEHICYD FKDAQMMDLM
310 320 330 340 350
RPSLEESFVI QSQEVALDYL GKRGSTMGTR EQRIKFAREV LQKEMLPHVS
360 370 380 390 400
VAEFYETKKA FYFGYITHRL LLASLERRPL DDRDHFANKR LDLAGPLLGT
410 420 430 440 450
LFRQLFKKLT KDVRLYLQRC IDKDKEFIAS SAVKSKTITS GLKYSLATGN
460 470 480 490 500
WGSSKSGGTK SGVAQVLNRL TFASTLSHLR RLNTPIGREG KLAKPRQLHN
510 520 530 540 550
THWGIVCPSE TPEGQACGLV KNLAMMSYIS VGSASQPILE FLEEWTTENL
560 570 580 590 600
EEISDLSSIF SATKIFVNGM WVGIHHQPDK LLSTLRLLRR CGDVSVEVSV
610 620 630 640 650
VRDIREKELR LYTDPGRCCR PLFVVQDNKV QIKKQHINKL INNDEYKWQD
660 670 680 690 700
LLSEGIVEYI DAEEEETVLI AMTPEDLVPM PNEQIVHTYT HCEIHPSMIL
710 720 730 740 750
GICCSIIPFP DHNQSPRNTY QAAMGKQAMG VYITNYQLRM DTMAHVLFYP
760 770 780 790 800
QKPLVTTRSM EYLHFRELPA GQNVCVAIAC YSGYNQEDSV ILNQSAIDRG
810 820 830 840 850
LFRSMFYRAY KDEQKKQTSL MEEVFEKPER DTCAGMRHGS YEKIDDDGLV
860 870 880 890 900
APGVRVAGDD IIIGKTTPLP PSDDDLGPKT RRHTKRDSST ALRSSETGIV
910 920 930 940 950
DQVILTTSGE GFKFCKVRVR SMRVPQIGDK FSSRHGQKGT CGMAYRQEDL
960 970 980 990 1000
PFTVEGIVPD IIVNPHAIPS RMTIGQLIEC LLGKVSASTG DEGDATPFTD
1010 1020 1030 1040 1050
VTVEAISQAL HKIGYQMTGH EVMYNGHTGR RMDAQIFIGP TYYQRLKHMV
1060 1070 1080 1090 1100
DDKIHSRSRG PVQILTRQPV EGRSRDGGLR FGEMERDCMI SHGAAQFLKE
1110 1120 1130 1140 1150
RLFDQSDSYR VHICDICGLI AIANLKKNSF ECRRCKNKTQ ISQIRMPYAA
1160 1170
KLLFQELMSM SIAPRMFTQT
Length:1,170
Mass (Da):132,422
Last modified:May 24, 2005 - v1
Checksum:iDBDE1126B4DAB5C6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000109 Genomic DNA. Translation: EAL63310.1.
RefSeqiXP_636812.1. XM_631720.1.

Genome annotation databases

EnsemblProtistsiDDB0216277; DDB0216277; DDB_G0288257.
GeneIDi8626529.
KEGGiddi:DDB_G0288257.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000109 Genomic DNA. Translation: EAL63310.1.
RefSeqiXP_636812.1. XM_631720.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB0216277.

Proteomic databases

PaxDbiQ54J75.
PRIDEiQ54J75.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiDDB0216277; DDB0216277; DDB_G0288257.
GeneIDi8626529.
KEGGiddi:DDB_G0288257.

Organism-specific databases

dictyBaseiDDB_G0288257. rpb2.

Phylogenomic databases

eggNOGiKOG0214. Eukaryota.
COG0085. LUCA.
InParanoidiQ54J75.
KOiK03010.
OMAiRTQPHFE.
PhylomeDBiQ54J75.

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

PROiQ54J75.

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

  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.

Entry informationi

Entry nameiRPB2_DICDI
AccessioniPrimary (citable) accession number: Q54J75
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 8, 2008
Last sequence update: May 24, 2005
Last modified: June 8, 2016
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

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. 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.