RPB2_DICDI
ID RPB2_DICDI Reviewed; 1170 AA.
AC Q54J75;
DT 08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=DNA-directed RNA polymerase II subunit rpb2;
DE Short=RNA polymerase II subunit 2;
DE Short=RNA polymerase II subunit B2;
DE EC=2.7.7.6;
GN Name=polr2b; Synonyms=rpb2; ORFNames=DDB_G0288257;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
CC -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of
CC DNA into RNA using the four ribonucleoside triphosphates as substrates.
CC Second largest component of RNA polymerase II which synthesizes mRNA
CC precursors and many functional non-coding RNAs. Proposed to contribute
CC to the polymerase catalytic activity and forms the polymerase active
CC center together with the largest subunit. Pol II is the central
CC component of the basal RNA polymerase II transcription machinery. It is
CC composed of mobile elements that move relative to each other. rpb2 is
CC part of the core element with the central large cleft, the clamp
CC element that moves to open and close the cleft and the jaws that are
CC thought to grab the incoming DNA template (By similarity).
CC {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.6;
CC -!- SUBUNIT: Component of the RNA polymerase II (Pol II) complex.
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- MISCELLANEOUS: The binding of ribonucleoside triphosphate to the RNA
CC polymerase II transcribing complex probably involves a two-step
CC mechanism. The initial binding seems to occur at the entry (E) site and
CC involves a magnesium ion coordinated by three conserved aspartate
CC residues of the two largest RNA Pol II subunits (By similarity).
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the RNA polymerase beta chain family.
CC {ECO:0000305}.
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DR EMBL; AAFI02000109; EAL63310.1; -; Genomic_DNA.
DR RefSeq; XP_636812.1; XM_631720.1.
DR AlphaFoldDB; Q54J75; -.
DR SMR; Q54J75; -.
DR STRING; 44689.DDB0216277; -.
DR PaxDb; Q54J75; -.
DR EnsemblProtists; EAL63310; EAL63310; DDB_G0288257.
DR GeneID; 8626529; -.
DR KEGG; ddi:DDB_G0288257; -.
DR dictyBase; DDB_G0288257; rpb2.
DR eggNOG; KOG0214; Eukaryota.
DR HOGENOM; CLU_000524_5_2_1; -.
DR InParanoid; Q54J75; -.
DR OMA; RDLHGTH; -.
DR PhylomeDB; Q54J75; -.
DR Reactome; R-DDI-113418; Formation of the Early Elongation Complex.
DR Reactome; R-DDI-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-DDI-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-DDI-6782135; Dual incision in TC-NER.
DR Reactome; R-DDI-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-DDI-6796648; TP53 Regulates Transcription of DNA Repair Genes.
DR Reactome; R-DDI-6803529; FGFR2 alternative splicing.
DR Reactome; R-DDI-6807505; RNA polymerase II transcribes snRNA genes.
DR Reactome; R-DDI-72086; mRNA Capping.
DR Reactome; R-DDI-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-DDI-72165; mRNA Splicing - Minor Pathway.
DR Reactome; R-DDI-73776; RNA Polymerase II Promoter Escape.
DR Reactome; R-DDI-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
DR Reactome; R-DDI-75953; RNA Polymerase II Transcription Initiation.
DR Reactome; R-DDI-75955; RNA Polymerase II Transcription Elongation.
DR Reactome; R-DDI-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.
DR Reactome; R-DDI-77075; RNA Pol II CTD phosphorylation and interaction with CE.
DR Reactome; R-DDI-9018519; Estrogen-dependent gene expression.
DR PRO; PR:Q54J75; -.
DR Proteomes; UP000002195; Chromosome 5.
DR GO; GO:0005665; C:RNA polymerase II, core complex; ISS:dictyBase.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; ISS:dictyBase.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0032549; F:ribonucleoside binding; IEA:InterPro.
DR GO; GO:0006366; P:transcription by RNA polymerase II; ISS:dictyBase.
DR CDD; cd00653; RNA_pol_B_RPB2; 1.
DR Gene3D; 2.40.270.10; -; 1.
DR Gene3D; 2.40.50.150; -; 1.
DR Gene3D; 3.90.1110.10; -; 1.
DR InterPro; IPR015712; DNA-dir_RNA_pol_su2.
DR InterPro; IPR007120; DNA-dir_RNAP_su2_dom.
DR InterPro; IPR037033; DNA-dir_RNAP_su2_hyb_sf.
DR InterPro; IPR007121; RNA_pol_bsu_CS.
DR InterPro; IPR007644; RNA_pol_bsu_protrusion.
DR InterPro; IPR007642; RNA_pol_Rpb2_2.
DR InterPro; IPR037034; RNA_pol_Rpb2_2_sf.
DR InterPro; IPR007645; RNA_pol_Rpb2_3.
DR InterPro; IPR007646; RNA_pol_Rpb2_4.
DR InterPro; IPR007647; RNA_pol_Rpb2_5.
DR InterPro; IPR007641; RNA_pol_Rpb2_7.
DR InterPro; IPR014724; RNA_pol_RPB2_OB-fold.
DR PANTHER; PTHR20856; PTHR20856; 1.
DR Pfam; PF04563; RNA_pol_Rpb2_1; 1.
DR Pfam; PF04561; RNA_pol_Rpb2_2; 1.
DR Pfam; PF04565; RNA_pol_Rpb2_3; 1.
DR Pfam; PF04566; RNA_pol_Rpb2_4; 1.
DR Pfam; PF04567; RNA_pol_Rpb2_5; 1.
DR Pfam; PF00562; RNA_pol_Rpb2_6; 1.
DR Pfam; PF04560; RNA_pol_Rpb2_7; 1.
DR PROSITE; PS01166; RNA_POL_BETA; 1.
PE 3: Inferred from homology;
KW DNA-directed RNA polymerase; Magnesium; Metal-binding;
KW Nucleotidyltransferase; Nucleus; Reference proteome; Transcription;
KW Transferase; Zinc; Zinc-finger.
FT CHAIN 1..1170
FT /note="DNA-directed RNA polymerase II subunit rpb2"
FT /id="PRO_0000328242"
FT ZN_FING 1114..1135
FT /note="C4-type"
FT REGION 864..893
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 875..890
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 788
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="ligand shared with RPB1"
FT /evidence="ECO:0000250"
FT BINDING 1114
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1117
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1132
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
FT BINDING 1135
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1170 AA; 132422 MW; DBDE1126B4DAB5C6 CRC64;
MSDYMMNDDS QDNPHADISQ EDVWTVISAY FQEKGLVRQQ LDSFDEFIQN TMQEIIDESP
PITLRPESQH HPGQAVVSNN VSTFSVKFGQ IYLSKPTAEI DGVSQQVTPN QARIRNLTYS
APLFVDITKT VMTGSKSKGD ERRTDEVLKR IFIGKVPIML RSQYCMLNEA DDRDLTTMGE
CSFDQGGYFI INGSEKVLIA QEKMNNNHVY VFKKSPPSKY SYVAEIRSCQ ETGSRPTSTM
YLKMLHNTNK GPVGIKATVP YIKQDVPVII VFRALGFVAD KDILEHICYD FKDAQMMDLM
RPSLEESFVI QSQEVALDYL GKRGSTMGTR EQRIKFAREV LQKEMLPHVS VAEFYETKKA
FYFGYITHRL LLASLERRPL DDRDHFANKR LDLAGPLLGT LFRQLFKKLT KDVRLYLQRC
IDKDKEFIAS SAVKSKTITS GLKYSLATGN WGSSKSGGTK SGVAQVLNRL TFASTLSHLR
RLNTPIGREG KLAKPRQLHN THWGIVCPSE TPEGQACGLV KNLAMMSYIS VGSASQPILE
FLEEWTTENL EEISDLSSIF SATKIFVNGM WVGIHHQPDK LLSTLRLLRR CGDVSVEVSV
VRDIREKELR LYTDPGRCCR PLFVVQDNKV QIKKQHINKL INNDEYKWQD LLSEGIVEYI
DAEEEETVLI AMTPEDLVPM PNEQIVHTYT HCEIHPSMIL GICCSIIPFP DHNQSPRNTY
QAAMGKQAMG VYITNYQLRM DTMAHVLFYP QKPLVTTRSM EYLHFRELPA GQNVCVAIAC
YSGYNQEDSV ILNQSAIDRG LFRSMFYRAY KDEQKKQTSL MEEVFEKPER DTCAGMRHGS
YEKIDDDGLV APGVRVAGDD IIIGKTTPLP PSDDDLGPKT RRHTKRDSST ALRSSETGIV
DQVILTTSGE GFKFCKVRVR SMRVPQIGDK FSSRHGQKGT CGMAYRQEDL PFTVEGIVPD
IIVNPHAIPS RMTIGQLIEC LLGKVSASTG DEGDATPFTD VTVEAISQAL HKIGYQMTGH
EVMYNGHTGR RMDAQIFIGP TYYQRLKHMV DDKIHSRSRG PVQILTRQPV EGRSRDGGLR
FGEMERDCMI SHGAAQFLKE RLFDQSDSYR VHICDICGLI AIANLKKNSF ECRRCKNKTQ
ISQIRMPYAA KLLFQELMSM SIAPRMFTQT
