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Protein

DNA-directed RNA polymerase II subunit rpb4

Gene

rpb4

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-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 similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription

Enzyme and pathway databases

ReactomeiR-SPO-113418. Formation of the Early Elongation Complex.
R-SPO-674695. RNA Polymerase II Pre-transcription Events.
R-SPO-6781823. Formation of TC-NER Pre-Incision Complex.
R-SPO-6782135. Dual incision in TC-NER.
R-SPO-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SPO-72086. mRNA Capping.
R-SPO-72165. mRNA Splicing - Minor Pathway.
R-SPO-73776. RNA Polymerase II Promoter Escape.
R-SPO-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SPO-75953. RNA Polymerase II Transcription Initiation.
R-SPO-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SPO-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit rpb4
Short name:
RNA polymerase II subunit B4
Gene namesi
Name:rpb4
ORF Names:SPBC337.14
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:SPBC337.14.
PomBaseiSPBC337.14. rpb4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasmic mRNA processing body Source: GO_Central
  • DNA-directed RNA polymerase II, core complex Source: GO_Central
  • DNA-directed RNA polymerase II, holoenzyme Source: PomBase
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 135135DNA-directed RNA polymerase II subunit rpb4PRO_0000073983Add
BLAST

Proteomic databases

MaxQBiO74825.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits. RPB4 and RPB7 form a Pol II subcomplex (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
med8O946463EBI-697320,EBI-1533413

GO - Molecular functioni

Protein-protein interaction databases

BioGridi277526. 12 interactions.
IntActiO74825. 3 interactions.
MINTiMINT-4681017.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3H0GX-ray3.65D/P1-135[»]
ProteinModelPortaliO74825.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO74825.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000195281.
InParanoidiO74825.
KOiK03012.
OMAiQTMRKFQ.
OrthoDBiEOG092C5NLC.
PhylomeDBiO74825.

Family and domain databases

InterProiIPR010997. HRDC-like.
IPR005574. RNA_pol_II_Rpb4.
IPR006590. RNA_pol_II_Rpb4_core.
[Graphical view]
PfamiPF03874. RNA_pol_Rpb4. 1 hit.
[Graphical view]
SMARTiSM00657. RPOL4c. 1 hit.
[Graphical view]
SUPFAMiSSF47819. SSF47819. 1 hit.

Sequencei

Sequence statusi: Complete.

O74825-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPRAIFEEDA AQLKLGPEFE NEDMLTVSEA KILIETVLAQ RARETNGEIP
60 70 80 90 100
MTDVMKKTVA YFNVFARFKT AEATYACERI LGNRFHKFER AQLGTLCCED
110 120 130
AEEARTLIPS LANKIDDQNL QGILDELSTL RKFQD
Length:135
Mass (Da):15,362
Last modified:November 1, 1998 - v1
Checksum:i61C98593A01C1E04
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB019575 Genomic DNA. Translation: BAA85621.1.
AF149308 mRNA. Translation: AAF62856.1.
CU329671 Genomic DNA. Translation: CAA21284.1.
PIRiT40267.
RefSeqiNP_595415.1. NM_001021322.2.

Genome annotation databases

EnsemblFungiiSPBC337.14.1; SPBC337.14.1:pep; SPBC337.14.
GeneIDi2541011.
KEGGispo:SPBC337.14.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB019575 Genomic DNA. Translation: BAA85621.1.
AF149308 mRNA. Translation: AAF62856.1.
CU329671 Genomic DNA. Translation: CAA21284.1.
PIRiT40267.
RefSeqiNP_595415.1. NM_001021322.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3H0GX-ray3.65D/P1-135[»]
ProteinModelPortaliO74825.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi277526. 12 interactions.
IntActiO74825. 3 interactions.
MINTiMINT-4681017.

Proteomic databases

MaxQBiO74825.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPBC337.14.1; SPBC337.14.1:pep; SPBC337.14.
GeneIDi2541011.
KEGGispo:SPBC337.14.

Organism-specific databases

EuPathDBiFungiDB:SPBC337.14.
PomBaseiSPBC337.14. rpb4.

Phylogenomic databases

HOGENOMiHOG000195281.
InParanoidiO74825.
KOiK03012.
OMAiQTMRKFQ.
OrthoDBiEOG092C5NLC.
PhylomeDBiO74825.

Enzyme and pathway databases

ReactomeiR-SPO-113418. Formation of the Early Elongation Complex.
R-SPO-674695. RNA Polymerase II Pre-transcription Events.
R-SPO-6781823. Formation of TC-NER Pre-Incision Complex.
R-SPO-6782135. Dual incision in TC-NER.
R-SPO-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SPO-72086. mRNA Capping.
R-SPO-72165. mRNA Splicing - Minor Pathway.
R-SPO-73776. RNA Polymerase II Promoter Escape.
R-SPO-73779. RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.
R-SPO-75953. RNA Polymerase II Transcription Initiation.
R-SPO-76042. RNA Polymerase II Transcription Initiation And Promoter Clearance.
R-SPO-77075. RNA Pol II CTD phosphorylation and interaction with CE.

Miscellaneous databases

EvolutionaryTraceiO74825.
PROiO74825.

Family and domain databases

InterProiIPR010997. HRDC-like.
IPR005574. RNA_pol_II_Rpb4.
IPR006590. RNA_pol_II_Rpb4_core.
[Graphical view]
PfamiPF03874. RNA_pol_Rpb4. 1 hit.
[Graphical view]
SMARTiSM00657. RPOL4c. 1 hit.
[Graphical view]
SUPFAMiSSF47819. SSF47819. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRPB4_SCHPO
AccessioniPrimary (citable) accession number: O74825
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: November 1, 1998
Last modified: September 7, 2016
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  3. 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.