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Protein

DNA-directed RNA polymerase II subunit RPB4

Gene

POLR2D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. 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. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double-stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA (By similarity).By similarity1 Publication

GO - Molecular functioni

  • DNA-directed 5'-3' RNA polymerase activity Source: UniProtKB
  • nucleotide binding Source: InterPro
  • translation initiation factor binding Source: GO_Central

GO - Biological processi

Keywordsi

Biological processTranscription

Enzyme and pathway databases

ReactomeiR-HSA-112382 Formation of RNA Pol II elongation complex
R-HSA-113418 Formation of the Early Elongation Complex
R-HSA-167152 Formation of HIV elongation complex in the absence of HIV Tat
R-HSA-167158 Formation of the HIV-1 Early Elongation Complex
R-HSA-167160 RNA Pol II CTD phosphorylation and interaction with CE during HIV infection
R-HSA-167161 HIV Transcription Initiation
R-HSA-167162 RNA Polymerase II HIV Promoter Escape
R-HSA-167172 Transcription of the HIV genome
R-HSA-167200 Formation of HIV-1 elongation complex containing HIV-1 Tat
R-HSA-167238 Pausing and recovery of Tat-mediated HIV elongation
R-HSA-167242 Abortive elongation of HIV-1 transcript in the absence of Tat
R-HSA-167243 Tat-mediated HIV elongation arrest and recovery
R-HSA-167246 Tat-mediated elongation of the HIV-1 transcript
R-HSA-167287 HIV elongation arrest and recovery
R-HSA-167290 Pausing and recovery of HIV elongation
R-HSA-168325 Viral Messenger RNA Synthesis
R-HSA-203927 MicroRNA (miRNA) biogenesis
R-HSA-452723 Transcriptional regulation of pluripotent stem cells
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-5601884 PIWI-interacting RNA (piRNA) biogenesis
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-6781823 Formation of TC-NER Pre-Incision Complex
R-HSA-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
R-HSA-6782135 Dual incision in TC-NER
R-HSA-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-HSA-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-HSA-6803529 FGFR2 alternative splicing
R-HSA-6807505 RNA polymerase II transcribes snRNA genes
R-HSA-72086 mRNA Capping
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-73776 RNA Polymerase II Promoter Escape
R-HSA-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-HSA-75953 RNA Polymerase II Transcription Initiation
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-HSA-77075 RNA Pol II CTD phosphorylation and interaction with CE
R-HSA-8851708 Signaling by FGFR2 IIIa TM
R-HSA-9018519 Estrogen-dependent gene expression

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB4
Short name:
RNA polymerase II subunit B4
Alternative name(s):
DNA-directed RNA polymerase II subunit D
RNA polymerase II 16 kDa subunit
Short name:
RPB16
Gene namesi
Name:POLR2D
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

EuPathDBiHostDB:ENSG00000144231.10
HGNCiHGNC:9191 POLR2D
MIMi606017 gene
neXtProtiNX_O15514

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi5433
OpenTargetsiENSG00000144231
PharmGKBiPA33511

Polymorphism and mutation databases

BioMutaiPOLR2D

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000739811 – 142DNA-directed RNA polymerase II subunit RPB4Add BLAST142

Proteomic databases

EPDiO15514
MaxQBiO15514
PaxDbiO15514
PeptideAtlasiO15514
PRIDEiO15514
ProteomicsDBi48705

PTM databases

iPTMnetiO15514
PhosphoSitePlusiO15514

Expressioni

Gene expression databases

BgeeiENSG00000144231
CleanExiHS_POLR2D
ExpressionAtlasiO15514 baseline and differential
GenevisibleiO15514 HS

Organism-specific databases

HPAiHPA034694
HPA046092

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. RPB4 and RPB7 form a subcomplex that protrudes from the 10-subunit Pol II core complex.1 Publication

GO - Molecular functioni

Protein-protein interaction databases

BioGridi111429, 73 interactors
CORUMiO15514
DIPiDIP-32912N
IntActiO15514, 19 interactors
STRINGi9606.ENSP00000272645

Structurei

Secondary structure

1142
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi17 – 19Combined sources3
Beta strandi24 – 28Combined sources5
Helixi34 – 49Combined sources16
Helixi59 – 70Combined sources12
Helixi77 – 88Combined sources12
Helixi94 – 103Combined sources10
Helixi108 – 114Combined sources7
Helixi116 – 118Combined sources3
Turni119 – 121Combined sources3
Helixi124 – 137Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2C35X-ray2.70A/C/E/G1-142[»]
5IY6electron microscopy7.20D1-142[»]
5IY7electron microscopy8.60D1-142[»]
5IY8electron microscopy7.90D1-142[»]
5IY9electron microscopy6.30D1-142[»]
5IYAelectron microscopy5.40D1-142[»]
5IYBelectron microscopy3.90D1-142[»]
5IYCelectron microscopy3.90D1-142[»]
5IYDelectron microscopy3.90D1-142[»]
ProteinModelPortaliO15514
SMRiO15514
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO15514

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG2351 Eukaryota
COG5250 LUCA
GeneTreeiENSGT00390000004912
HOGENOMiHOG000195281
HOVERGENiHBG002800
InParanoidiO15514
KOiK03012
OMAiQTMRKFQ
OrthoDBiEOG091G06WT
PhylomeDBiO15514
TreeFamiTF103039

Family and domain databases

Gene3Di1.20.1250.40, 1 hit
InterProiView protein in InterPro
IPR010997 HRDC-like_sf
IPR006590 RNA_pol_Rpb4/RPC9_core
IPR005574 RPB4/RPC9
IPR038324 Rpb4/RPC9_sf
PfamiView protein in Pfam
PF03874 RNA_pol_Rpb4, 1 hit
SMARTiView protein in SMART
SM00657 RPOL4c, 1 hit
SUPFAMiSSF47819 SSF47819, 1 hit

Sequencei

Sequence statusi: Complete.

O15514-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAAGGSDPRA GDVEEDASQL IFPKEFETAE TLLNSEVHML LEHRKQQNES
60 70 80 90 100
AEDEQELSEV FMKTLNYTAR FSRFKNRETI ASVRSLLLQK KLHKFELACL
110 120 130 140
ANLCPETAEE SKALIPSLEG RFEDEELQQI LDDIQTKRSF QY
Length:142
Mass (Da):16,311
Last modified:January 1, 1998 - v1
Checksum:i8A670386C433BE93
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89387 Genomic DNA Translation: AAC52056.1
U85510 mRNA Translation: AAC80226.1
BC017205 mRNA Translation: AAH17205.1
BC093795 mRNA Translation: AAH93795.1
BC093797 mRNA Translation: AAH93797.1
CCDSiCCDS2151.1
RefSeqiNP_004796.1, NM_004805.3
UniGeneiHs.715348

Genome annotation databases

EnsembliENST00000272645; ENSP00000272645; ENSG00000144231
GeneIDi5433
KEGGihsa:5433
UCSCiuc002tpj.4 human

Similar proteinsi

Entry informationi

Entry nameiRPB4_HUMAN
AccessioniPrimary (citable) accession number: O15514
Secondary accession number(s): Q52LT4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 1, 1998
Last modified: June 20, 2018
This is version 173 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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