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Protein

DNA-directed RNA polymerase II subunit RPB9

Gene

RPB9

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template. Involved in the regulation of transcription elongation. Involved in DNA repair of damage in the transcribed strand. Mediates a transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER).1 Publication

Miscellaneous

Present with 2440 molecules/cell in log phase SD medium.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi7Zinc 11 Publication3 Publications1
Metal bindingi10Zinc 11 Publication3 Publications1
Metal bindingi29Zinc 11 Publication3 Publications1
Metal bindingi32Zinc 11 Publication3 Publications1
Metal bindingi75Zinc 21 Publication3 Publications1
Metal bindingi78Zinc 21 Publication3 Publications1
Metal bindingi103Zinc 21 Publication3 Publications1
Metal bindingi106Zinc 21 Publication3 Publications1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri7 – 32C4-typeSequence analysisAdd BLAST26
Zinc fingeri71 – 111TFIIS-typePROSITE-ProRule annotationAdd BLAST41

GO - Molecular functioni

GO - Biological processi

  • maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter Source: SGD
  • mRNA cleavage Source: InterPro
  • transcription, RNA-templated Source: GOC
  • transcription by RNA polymerase II Source: SGD
  • transcription-coupled nucleotide-excision repair Source: SGD
  • transcription initiation from RNA polymerase II promoter Source: SGD

Keywordsi

Biological processDNA damage, DNA repair, Transcription
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-30573-MONOMER
ReactomeiR-SCE-113418 Formation of the Early Elongation Complex
R-SCE-674695 RNA Polymerase II Pre-transcription Events
R-SCE-6781823 Formation of TC-NER Pre-Incision Complex
R-SCE-6782135 Dual incision in TC-NER
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-SCE-6807505 RNA polymerase II transcribes snRNA genes
R-SCE-72086 mRNA Capping
R-SCE-72165 mRNA Splicing - Minor Pathway
R-SCE-73776 RNA Polymerase II Promoter Escape
R-SCE-73779 RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
R-SCE-75953 RNA Polymerase II Transcription Initiation
R-SCE-76042 RNA Polymerase II Transcription Initiation And Promoter Clearance
R-SCE-77075 RNA Pol II CTD phosphorylation and interaction with CE
R-SCE-9018519 Estrogen-dependent gene expression

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase II subunit RPB9
Short name:
RNA polymerase II subunit B9
Alternative name(s):
B12.6
DNA-directed RNA polymerase II 14.2 kDa polypeptide
DNA-directed RNA polymerase II subunit 9
Gene namesi
Name:RPB9
Ordered Locus Names:YGL070C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGL070C
SGDiS000003038 RPB9

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole 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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001214741 – 122DNA-directed RNA polymerase II subunit RPB9Add BLAST122

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei40PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP27999
PRIDEiP27999

PTM databases

iPTMnetiP27999

Interactioni

Subunit structurei

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

Binary interactionsi

WithEntry#Exp.IntActNotes
RPB8P204363EBI-15798,EBI-15794

Protein-protein interaction databases

BioGridi33178, 91 interactors
ComplexPortaliCPX-2662 DNA-directed RNA polymerase II complex
DIPiDIP-610N
IntActiP27999, 20 interactors
MINTiP27999
STRINGi4932.YGL070C

Structurei

Secondary structure

1122
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 10Combined sources3
Beta strandi15 – 19Combined sources5
Turni20 – 23Combined sources4
Beta strandi24 – 28Combined sources5
Beta strandi30 – 33Combined sources4
Beta strandi35 – 37Combined sources3
Beta strandi41 – 49Combined sources9
Turni52 – 57Combined sources6
Helixi62 – 64Combined sources3
Beta strandi66 – 68Combined sources3
Turni76 – 78Combined sources3
Beta strandi83 – 87Combined sources5
Beta strandi92 – 94Combined sources3
Beta strandi99 – 103Combined sources5
Turni104 – 106Combined sources3
Beta strandi109 – 111Combined sources3
Beta strandi114 – 116Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1I3QX-ray3.10I1-122[»]
1I50X-ray2.80I1-122[»]
1I6HX-ray3.30I1-122[»]
1K83X-ray2.80I1-122[»]
1NIKX-ray4.10I1-122[»]
1NT9X-ray4.20I1-122[»]
1PQVX-ray3.80I1-122[»]
1R5UX-ray4.50I1-122[»]
1R9SX-ray4.25I1-122[»]
1R9TX-ray3.50I1-122[»]
1SFOX-ray3.61I1-122[»]
1TWAX-ray3.20I1-122[»]
1TWCX-ray3.00I1-122[»]
1TWFX-ray2.30I1-122[»]
1TWGX-ray3.30I1-122[»]
1TWHX-ray3.40I1-122[»]
1WCMX-ray3.80I1-122[»]
1Y1VX-ray3.80I1-122[»]
1Y1WX-ray4.00I1-122[»]
1Y1YX-ray4.00I1-122[»]
1Y77X-ray4.50I1-122[»]
2B63X-ray3.80I1-122[»]
2B8KX-ray4.15I1-122[»]
2E2HX-ray3.95I1-122[»]
2E2IX-ray3.41I1-122[»]
2E2JX-ray3.50I1-122[»]
2JA5X-ray3.80I1-122[»]
2JA6X-ray4.00I1-122[»]
2JA7X-ray3.80I/U1-122[»]
2JA8X-ray3.80I1-122[»]
2NVQX-ray2.90I1-122[»]
2NVTX-ray3.36I1-122[»]
2NVXX-ray3.60I1-122[»]
2NVYX-ray3.40I1-122[»]
2NVZX-ray4.30I1-122[»]
2R7ZX-ray3.80I1-122[»]
2R92X-ray3.80I1-122[»]
2R93X-ray4.00I1-122[»]
2VUMX-ray3.40I1-122[»]
2YU9X-ray3.40I1-122[»]
3CQZX-ray2.80I1-122[»]
3FKIX-ray3.88I1-122[»]
3GTGX-ray3.78I1-122[»]
3GTJX-ray3.42I1-122[»]
3GTKX-ray3.80I1-122[»]
3GTLX-ray3.38I1-122[»]
3GTMX-ray3.80I1-122[»]
3GTOX-ray4.00I1-122[»]
3GTPX-ray3.90I1-122[»]
3GTQX-ray3.80I1-122[»]
3H3VX-ray4.00J1-122[»]
3HOUX-ray3.20I/U1-122[»]
3HOVX-ray3.50I1-122[»]
3HOWX-ray3.60I1-122[»]
3HOXX-ray3.65I1-122[»]
3HOYX-ray3.40I1-122[»]
3HOZX-ray3.65I1-122[»]
3I4MX-ray3.70I1-122[»]
3I4NX-ray3.90I1-122[»]
3J0Kelectron microscopy36.00I1-122[»]
3J1Nelectron microscopy16.00I1-122[»]
3K1FX-ray4.30I1-122[»]
3K7AX-ray3.80I1-122[»]
3M3YX-ray3.18I1-122[»]
3M4OX-ray3.57I1-122[»]
3PO2X-ray3.30I1-122[»]
3PO3X-ray3.30I1-122[»]
3QT1X-ray4.30I1-87[»]
3RZDX-ray3.30I1-122[»]
3RZOX-ray3.00I1-122[»]
3S14X-ray2.85I1-122[»]
3S15X-ray3.30I1-122[»]
3S16X-ray3.24I1-122[»]
3S17X-ray3.20I1-122[»]
3S1MX-ray3.13I1-122[»]
3S1NX-ray3.10I1-122[»]
3S1QX-ray3.30I1-122[»]
3S1RX-ray3.20I1-122[»]
3S2DX-ray3.20I1-122[»]
3S2HX-ray3.30I1-122[»]
4A3BX-ray3.50I1-122[»]
4A3CX-ray3.50I1-122[»]
4A3DX-ray3.40I1-122[»]
4A3EX-ray3.40I1-122[»]
4A3FX-ray3.50I1-122[»]
4A3GX-ray3.50I1-122[»]
4A3IX-ray3.80I1-122[»]
4A3JX-ray3.70I1-122[»]
4A3KX-ray3.50I1-122[»]
4A3LX-ray3.50I1-122[»]
4A3MX-ray3.90I1-122[»]
4A93X-ray3.40I1-122[»]
4BBRX-ray3.40I1-122[»]
4BBSX-ray3.60I1-122[»]
4BXXX-ray3.28I1-122[»]
4BXZX-ray4.80I1-122[»]
4BY1X-ray3.60I1-122[»]
4BY7X-ray3.15I1-122[»]
4V1Melectron microscopy6.60I1-122[»]
4V1Nelectron microscopy7.80I1-122[»]
4V1Oelectron microscopy9.70I1-122[»]
4X67X-ray4.10I1-122[»]
4X6AX-ray3.96I1-122[»]
4Y52X-ray3.50I1-122[»]
4Y7NX-ray3.30I1-122[»]
5C3EX-ray3.70I1-122[»]
5C44X-ray3.95I1-120[»]
5C4AX-ray4.20I1-122[»]
5C4JX-ray4.00I1-122[»]
5C4XX-ray4.00I1-122[»]
5FMFelectron microscopy6.00I2-120[»]
5FYWelectron microscopy4.35I1-122[»]
5FZ5electron microscopy8.80I1-122[»]
5IP7X-ray3.52I2-120[»]
5IP9X-ray3.90I2-120[»]
5OQJelectron microscopy4.70I1-122[»]
5OQMelectron microscopy5.80I1-122[»]
5OT2X-ray3.20I1-122[»]
5SVAelectron microscopy15.30I1-122[»]
5U5QX-ray3.80I1-122[»]
5VVRelectron microscopy5.80I1-122[»]
5VVSelectron microscopy6.40I1-122[»]
6BLOX-ray3.40I1-122[»]
6BLPX-ray3.20I1-122[»]
6BM2X-ray3.40I1-122[»]
6BM4X-ray2.95I1-122[»]
6BQFX-ray3.35I1-122[»]
ProteinModelPortaliP27999
SMRiP27999
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP27999

Family & Domainsi

Sequence similaritiesi

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri7 – 32C4-typeSequence analysisAdd BLAST26
Zinc fingeri71 – 111TFIIS-typePROSITE-ProRule annotationAdd BLAST41

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00550000075063
HOGENOMiHOG000228134
InParanoidiP27999
KOiK03017
OMAiETRMILF
OrthoDBiEOG092C59RA

Family and domain databases

CDDicd10508 Zn-ribbon_RPB9, 1 hit
InterProiView protein in InterPro
IPR019761 DNA-dir_RNA_pol-M_15_CS
IPR001529 DNA-dir_RNA_pol_M/15kDasu
IPR012164 Rpa12/Rpb9/Rpc10/TFS
IPR034012 Zn_ribbon_RPB9_C
IPR001222 Znf_TFIIS
PfamiView protein in Pfam
PF02150 RNA_POL_M_15KD, 1 hit
PF01096 TFIIS_C, 1 hit
PIRSFiPIRSF005586 RNApol_RpoM, 1 hit
SMARTiView protein in SMART
SM00661 RPOL9, 1 hit
SM00440 ZnF_C2C2, 1 hit
PROSITEiView protein in PROSITE
PS01030 RNA_POL_M_15KD, 1 hit
PS00466 ZF_TFIIS_1, 1 hit
PS51133 ZF_TFIIS_2, 1 hit

Sequencei

Sequence statusi: Complete.

P27999-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTTFRFCRDC NNMLYPREDK ENNRLLFECR TCSYVEEAGS PLVYRHELIT
60 70 80 90 100
NIGETAGVVQ DIGSDPTLPR SDRECPKCHS RENVFFQSQQ RRKDTSMVLF
110 120
FVCLSCSHIF TSDQKNKRTQ FS
Length:122
Mass (Da):14,288
Last modified:August 1, 1992 - v1
Checksum:iA80D69678A722881
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M73060 Genomic DNA Translation: AAA34997.1
Z72592 Genomic DNA Translation: CAA96774.1
AY557799 Genomic DNA Translation: AAS56125.1
BK006941 Genomic DNA Translation: DAA08033.1
PIRiA41016 RNBY29
RefSeqiNP_011445.1, NM_001180935.1

Genome annotation databases

EnsemblFungiiYGL070C; YGL070C; YGL070C
GeneIDi852810
KEGGisce:YGL070C

Similar proteinsi

Entry informationi

Entry nameiRPB9_YEAST
AccessioniPrimary (citable) accession number: P27999
Secondary accession number(s): D6VU72
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: June 20, 2018
This is version 199 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

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