NRPB4_ARATH
ID NRPB4_ARATH Reviewed; 138 AA.
AC O48890;
DT 18-SEP-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 25-MAY-2022, entry version 132.
DE RecName: Full=DNA-directed RNA polymerase II subunit 4;
DE AltName: Full=15.9 kDa subunit of RNA polymerase II;
DE AltName: Full=DNA-directed RNA polymerase II subunit D;
GN Name=NRPB4; Synonyms=RPB15.9, RPB4; OrderedLocusNames=At5g09920;
GN ORFNames=MYH9.13;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], SUBUNIT, AND INTERACTION WITH NRPB7.
RX PubMed=9488692; DOI=10.1074/jbc.273.10.5631;
RA Larkin R.M., Guilfoyle T.J.;
RT "Two small subunits in Arabidopsis RNA polymerase II are related to yeast
RT RPB4 and RPB7 and interact with one another.";
RL J. Biol. Chem. 273:5631-5637(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10048488; DOI=10.1093/dnares/5.6.379;
RA Asamizu E., Sato S., Kaneko T., Nakamura Y., Kotani H., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VIII. Sequence
RT features of the regions of 1,081,958 bp covered by seventeen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:379-391(1998).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Kim C.J., Chen H., Quinitio C., Shinn P., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (MAY-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT, AND NOMENCLATURE.
RX PubMed=19110459; DOI=10.1016/j.molcel.2008.12.015;
RA Ream T.S., Haag J.R., Wierzbicki A.T., Nicora C.D., Norbeck A.D., Zhu J.K.,
RA Hagen G., Guilfoyle T.J., Pasa-Tolic L., Pikaard C.S.;
RT "Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal
RT their origins as specialized forms of RNA polymerase II.";
RL Mol. Cell 33:192-203(2009).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
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.
CC {ECO:0000269|PubMed:19110459}.
CC -!- SUBUNIT: Component of the RNA polymerase II complex consisting of at
CC least 12 subunits. Interacts with NRPB7. {ECO:0000269|PubMed:19110459,
CC ECO:0000269|PubMed:9488692}.
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; AF016511; AAB95261.1; -; mRNA.
DR EMBL; AB016893; BAB09413.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91467.1; -; Genomic_DNA.
DR EMBL; BT025500; ABF58918.1; -; mRNA.
DR EMBL; AK317113; BAH19801.1; -; mRNA.
DR EMBL; AY086086; AAM63291.1; -; mRNA.
DR RefSeq; NP_196554.1; NM_121029.3.
DR AlphaFoldDB; O48890; -.
DR SMR; O48890; -.
DR BioGRID; 16131; 12.
DR STRING; 3702.AT5G09920.1; -.
DR iPTMnet; O48890; -.
DR PaxDb; O48890; -.
DR PRIDE; O48890; -.
DR ProteomicsDB; 250566; -.
DR EnsemblPlants; AT5G09920.1; AT5G09920.1; AT5G09920.
DR GeneID; 830853; -.
DR Gramene; AT5G09920.1; AT5G09920.1; AT5G09920.
DR KEGG; ath:AT5G09920; -.
DR Araport; AT5G09920; -.
DR TAIR; locus:2178158; AT5G09920.
DR eggNOG; KOG2351; Eukaryota.
DR HOGENOM; CLU_110332_1_0_1; -.
DR InParanoid; O48890; -.
DR OMA; AQLGTLC; -.
DR OrthoDB; 1480091at2759; -.
DR PhylomeDB; O48890; -.
DR PRO; PR:O48890; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; O48890; baseline and differential.
DR Genevisible; O48890; AT.
DR GO; GO:0000932; C:P-body; IBA:GO_Central.
DR GO; GO:0005665; C:RNA polymerase II, core complex; IDA:UniProtKB.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IDA:TAIR.
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; TAS:TAIR.
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 1: Evidence at protein level;
KW Acetylation; DNA-directed RNA polymerase; Nucleus; Reference proteome;
KW Transcription.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..138
FT /note="DNA-directed RNA polymerase II subunit 4"
FT /id="PRO_0000423331"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22223895"
SQ SEQUENCE 138 AA; 15932 MW; 337D7290D7C5BE31 CRC64;
MSGEEEENAA ELKIGDEFLK AKCLMNCEVS LILEHKFEQL QQISEDPMNQ VSQVFEKSLQ
YVKRFSRYKN PDAVRQVREI LSRHQLTEFE LCVLGNLCPE TVEEAVAMVP SLKTKGRAHD
DEAIEKMLND LSLVKRFE
