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Protein

DNA-directed RNA polymerase II subunit RPB9

Gene

rpb9

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 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. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template (By similarity). Involved in the regulation of transcription elongation.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi7 – 71Zinc 1By similarity
Metal bindingi10 – 101Zinc 1By similarity
Metal bindingi29 – 291Zinc 1By similarity
Metal bindingi32 – 321Zinc 1By similarity
Metal bindingi75 – 751Zinc 2By similarity
Metal bindingi78 – 781Zinc 2By similarity
Metal bindingi103 – 1031Zinc 2By similarity
Metal bindingi106 – 1061Zinc 2By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri7 – 3226C4-typeSequence analysisAdd
BLAST
Zinc fingeri71 – 11141TFIIS-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Transcription

Keywords - Ligandi

Metal-binding, Zinc

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 RPB9
Short name:
RNA polymerase II subunit B9
Alternative name(s):
DNA-directed RNA polymerase II 13.2 kDa polypeptide
DNA-directed RNA polymerase II subunit 9
Gene namesi
Name:rpb9
ORF Names:SPAPYUG7.04c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome I

Organism-specific databases

EuPathDBiFungiDB:SPAPYUG7.04c.
PomBaseiSPAPYUG7.04c. rpb9.

Subcellular locationi

  • Nucleusnucleolus By similarity

GO - Cellular componenti

  • cytosol Source: PomBase
  • DNA-directed RNA polymerase II, core complex Source: PomBase
  • DNA-directed RNA polymerase II, holoenzyme Source: PomBase
  • nucleolus Source: UniProtKB-SubCell
  • 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 – 113113DNA-directed RNA polymerase II subunit RPB9PRO_0000121473Add
BLAST

Proteomic databases

MaxQBiO74635.

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.

Protein-protein interaction databases

BioGridi277972. 102 interactions.
MINTiMINT-1214577.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3H0GX-ray3.65I/U1-113[»]
ProteinModelPortaliO74635.
SMRiO74635. Positions 1-112.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO74635.

Family & Domainsi

Sequence similaritiesi

Contains 1 TFIIS-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri7 – 3226C4-typeSequence analysisAdd
BLAST
Zinc fingeri71 – 11141TFIIS-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOGENOMiHOG000228134.
InParanoidiO74635.
KOiK03017.
OMAiTLAHAKM.
OrthoDBiEOG092C59RA.
PhylomeDBiO74635.

Family and domain databases

InterProiIPR019761. DNA-dir_RNA_pol-M_15_CS.
IPR001529. DNA-dir_RNA_pol_M/15kDasu.
IPR012164. Rpa12/Rpb9/Rpc10/TFS.
IPR001222. Znf_TFIIS.
[Graphical view]
PfamiPF02150. RNA_POL_M_15KD. 1 hit.
PF01096. TFIIS_C. 1 hit.
[Graphical view]
PIRSFiPIRSF005586. RNApol_RpoM. 1 hit.
SMARTiSM00661. RPOL9. 1 hit.
SM00440. ZnF_C2C2. 1 hit.
[Graphical view]
PROSITEiPS01030. RNA_POL_M_15KD. 1 hit.
PS00466. ZF_TFIIS_1. 1 hit.
PS51133. ZF_TFIIS_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O74635-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSNFQYCIEC NNMLYPREDK VDRVLRLACR NCDYSEIAAT SKVYRHELQS
60 70 80 90 100
SNVENTTVSH DASTDPTLPR SDKECPRCHQ HEAVFYQTHS RRGDTMMTLI
110
YVCVHCGFAF EEQ
Length:113
Mass (Da):13,175
Last modified:November 1, 1998 - v1
Checksum:i55A1ABAF5832671A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB007988 Genomic DNA. Translation: BAA33021.1.
AF237418 Genomic DNA. Translation: AAL55660.1.
CU329670 Genomic DNA. Translation: CAB66313.1.
PIRiT43279.
RefSeqiNP_594705.1. NM_001020132.2.

Genome annotation databases

EnsemblFungiiSPAPYUG7.04c.1; SPAPYUG7.04c.1:pep; SPAPYUG7.04c.
GeneIDi2541470.
KEGGispo:SPAPYUG7.04c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB007988 Genomic DNA. Translation: BAA33021.1.
AF237418 Genomic DNA. Translation: AAL55660.1.
CU329670 Genomic DNA. Translation: CAB66313.1.
PIRiT43279.
RefSeqiNP_594705.1. NM_001020132.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3H0GX-ray3.65I/U1-113[»]
ProteinModelPortaliO74635.
SMRiO74635. Positions 1-112.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi277972. 102 interactions.
MINTiMINT-1214577.

Proteomic databases

MaxQBiO74635.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPAPYUG7.04c.1; SPAPYUG7.04c.1:pep; SPAPYUG7.04c.
GeneIDi2541470.
KEGGispo:SPAPYUG7.04c.

Organism-specific databases

EuPathDBiFungiDB:SPAPYUG7.04c.
PomBaseiSPAPYUG7.04c. rpb9.

Phylogenomic databases

HOGENOMiHOG000228134.
InParanoidiO74635.
KOiK03017.
OMAiTLAHAKM.
OrthoDBiEOG092C59RA.
PhylomeDBiO74635.

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

EvolutionaryTraceiO74635.
PROiO74635.

Family and domain databases

InterProiIPR019761. DNA-dir_RNA_pol-M_15_CS.
IPR001529. DNA-dir_RNA_pol_M/15kDasu.
IPR012164. Rpa12/Rpb9/Rpc10/TFS.
IPR001222. Znf_TFIIS.
[Graphical view]
PfamiPF02150. RNA_POL_M_15KD. 1 hit.
PF01096. TFIIS_C. 1 hit.
[Graphical view]
PIRSFiPIRSF005586. RNApol_RpoM. 1 hit.
SMARTiSM00661. RPOL9. 1 hit.
SM00440. ZnF_C2C2. 1 hit.
[Graphical view]
PROSITEiPS01030. RNA_POL_M_15KD. 1 hit.
PS00466. ZF_TFIIS_1. 1 hit.
PS51133. ZF_TFIIS_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPB9_SCHPO
AccessioniPrimary (citable) accession number: O74635
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 14, 2001
Last sequence update: November 1, 1998
Last modified: September 7, 2016
This is version 133 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.