RPB4_DICDI
ID RPB4_DICDI Reviewed; 155 AA.
AC Q54S04;
DT 08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 25-MAY-2022, entry version 94.
DE RecName: Full=DNA-directed RNA polymerase II subunit rpb4;
DE Short=RNA polymerase II subunit B4;
DE AltName: Full=DNA-directed RNA polymerase II subunit D;
GN Name=polr2d; Synonyms=rpb4; ORFNames=DDB_G0282739;
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 Component of RNA polymerase II which synthesizes mRNA precursors and
CC many functional non-coding RNAs. Pol II is the central component of the
CC basal RNA polymerase II transcription machinery. It is composed of
CC mobile elements that move relative to each other. RPB4 is part of a
CC subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and
CC RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems
CC to lock the clamp via RPB7 in the closed conformation thus preventing
CC double-stranded DNA to enter the active site cleft. The RPB4-RPB7
CC subcomplex binds single-stranded DNA and RNA (By similarity).
CC {ECO:0000250}.
CC -!- SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting
CC of 12 subunits. RPB4 and RPB7 form a subcomplex that protrudes from the
CC 10-subunit Pol II core complex (By similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the eukaryotic RPB4 RNA polymerase subunit
CC family. {ECO:0000305}.
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DR EMBL; AAFI02000047; EAL66229.1; -; Genomic_DNA.
DR RefSeq; XP_640235.1; XM_635143.1.
DR AlphaFoldDB; Q54S04; -.
DR SMR; Q54S04; -.
DR STRING; 44689.DDB0216294; -.
DR PaxDb; Q54S04; -.
DR EnsemblProtists; EAL66229; EAL66229; DDB_G0282739.
DR GeneID; 8623774; -.
DR KEGG; ddi:DDB_G0282739; -.
DR dictyBase; DDB_G0282739; rpb4.
DR eggNOG; KOG2351; Eukaryota.
DR HOGENOM; CLU_110332_2_1_1; -.
DR InParanoid; Q54S04; -.
DR OMA; AQLGTLC; -.
DR PhylomeDB; Q54S04; -.
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:Q54S04; -.
DR Proteomes; UP000002195; Chromosome 3.
DR GO; GO:0005737; C:cytoplasm; IDA:dictyBase.
DR GO; GO:0005634; C:nucleus; IDA:dictyBase.
DR GO; GO:0000932; C:P-body; IBA:GO_Central.
DR GO; GO:0005665; C:RNA polymerase II, core complex; ISS:dictyBase.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IGI:dictyBase.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0031369; F:translation initiation factor binding; IBA:GO_Central.
DR GO; GO:0031990; P:mRNA export from nucleus in response to heat stress; IBA:GO_Central.
DR GO; GO:0000288; P:nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; IBA:GO_Central.
DR GO; GO:0045948; P:positive regulation of translational initiation; IBA:GO_Central.
DR GO; GO:0034402; P:recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex; IBA:GO_Central.
DR GO; GO:0006366; P:transcription by RNA polymerase II; IGI:dictyBase.
DR GO; GO:0006367; P:transcription initiation from RNA polymerase II promoter; IBA:GO_Central.
DR Gene3D; 1.20.1250.40; -; 1.
DR InterPro; IPR010997; HRDC-like_sf.
DR InterPro; IPR006590; RNA_pol_Rpb4/RPC9_core.
DR InterPro; IPR045222; Rpb4-like.
DR InterPro; IPR005574; Rpb4/RPC9.
DR InterPro; IPR038324; Rpb4/RPC9_sf.
DR PANTHER; PTHR21297; PTHR21297; 1.
DR Pfam; PF03874; RNA_pol_Rpb4; 1.
DR SMART; SM00657; RPOL4c; 1.
DR SUPFAM; SSF47819; SSF47819; 1.
PE 3: Inferred from homology;
KW DNA-directed RNA polymerase; Nucleus; Reference proteome; Transcription.
FT CHAIN 1..155
FT /note="DNA-directed RNA polymerase II subunit rpb4"
FT /id="PRO_0000329431"
SQ SEQUENCE 155 AA; 17889 MW; EC6754553CF07C70 CRC64;
MTDPLIKRSG IQEEEDLTTL KFPRDLKDAK FLLNSEVAIL LEHRKGISES EGTEFPQNTL
LIHLYYNSIN DIIRTFHKTL AYAEKFSRYK NKTSIKQVRT ALSKQNLEEF EIASLANLCP
EISDEAKSLI PSLKKMEDDE LQAILDELSN LRKFN
