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Protein

DNA-directed RNA polymerase II subunit RPB3

Gene

RPB3

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. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination.1 Publication

Miscellaneous

Present with 10000 molecules/cell in log phase SD medium.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi86Zinc1
Metal bindingi88Zinc1
Metal bindingi92Zinc1
Metal bindingi95Zinc1

GO - Molecular functioni

GO - Biological processi

  • termination of RNA polymerase II transcription Source: SGD
  • transcription, RNA-templated Source: GOC
  • transcription by RNA polymerase II Source: SGD

Keywordsi

Biological processTranscription
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-31296-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 RPB3
Short name:
RNA polymerase II subunit 3
Short name:
RNA polymerase II subunit B3
Alternative name(s):
B44.5
DNA-directed RNA polymerase II 45 kDa polypeptide
Gene namesi
Name:RPB3
Ordered Locus Names:YIL021W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IX

Organism-specific databases

EuPathDBiFungiDB:YIL021W
SGDiS000001283 RPB3

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi9K → E: Transcript termination readthrough. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001327482 – 318DNA-directed RNA polymerase II subunit RPB3Add BLAST317

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP16370
PaxDbiP16370
PRIDEiP16370

PTM databases

iPTMnetiP16370

Interactioni

Subunit structurei

Component of the RNA polymerase II (Pol II) complex consisting of 12 subunits.3 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

Protein-protein interaction databases

BioGridi34967, 610 interactors
DIPiDIP-837N
IntActiP16370, 40 interactors
MINTiP16370
STRINGi4932.YIL021W

Structurei

Secondary structure

1318
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 7Combined sources3
Beta strandi11 – 13Combined sources3
Beta strandi15 – 18Combined sources4
Beta strandi21 – 25Combined sources5
Helixi27 – 39Combined sources13
Beta strandi43 – 54Combined sources12
Beta strandi56 – 58Combined sources3
Helixi60 – 68Combined sources9
Beta strandi72 – 74Combined sources3
Helixi77 – 79Combined sources3
Turni83 – 85Combined sources3
Beta strandi86 – 90Combined sources5
Turni93 – 95Combined sources3
Beta strandi96 – 104Combined sources9
Beta strandi107 – 109Combined sources3
Beta strandi111 – 114Combined sources4
Helixi115 – 117Combined sources3
Beta strandi118 – 120Combined sources3
Beta strandi128 – 132Combined sources5
Beta strandi137 – 139Combined sources3
Beta strandi142 – 147Combined sources6
Beta strandi152 – 162Combined sources11
Turni164 – 166Combined sources3
Helixi168 – 170Combined sources3
Beta strandi173 – 180Combined sources8
Helixi184 – 186Combined sources3
Helixi197 – 200Combined sources4
Helixi205 – 207Combined sources3
Beta strandi208 – 210Combined sources3
Beta strandi215 – 217Combined sources3
Beta strandi228 – 234Combined sources7
Beta strandi236 – 238Combined sources3
Helixi240 – 265Combined sources26

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1I3QX-ray3.10C1-318[»]
1I50X-ray2.80C1-318[»]
1I6HX-ray3.30C1-318[»]
1K83X-ray2.80C1-318[»]
1NIKX-ray4.10C1-318[»]
1NT9X-ray4.20C1-318[»]
1PQVX-ray3.80C1-318[»]
1R5UX-ray4.50C1-318[»]
1R9SX-ray4.25C1-318[»]
1R9TX-ray3.50C1-318[»]
1SFOX-ray3.61C1-318[»]
1TWAX-ray3.20C1-318[»]
1TWCX-ray3.00C1-318[»]
1TWFX-ray2.30C1-318[»]
1TWGX-ray3.30C1-318[»]
1TWHX-ray3.40C1-318[»]
1WCMX-ray3.80C1-318[»]
1Y1VX-ray3.80C1-318[»]
1Y1WX-ray4.00C1-318[»]
1Y1YX-ray4.00C1-318[»]
1Y77X-ray4.50C1-318[»]
2B63X-ray3.80C1-318[»]
2B8KX-ray4.15C1-318[»]
2E2HX-ray3.95C1-318[»]
2E2IX-ray3.41C1-318[»]
2E2JX-ray3.50C1-318[»]
2JA5X-ray3.80C1-318[»]
2JA6X-ray4.00C1-318[»]
2JA7X-ray3.80C/O1-318[»]
2JA8X-ray3.80C1-318[»]
2NVQX-ray2.90C1-318[»]
2NVTX-ray3.36C1-318[»]
2NVXX-ray3.60C1-318[»]
2NVYX-ray3.40C1-318[»]
2NVZX-ray4.30C1-318[»]
2R7ZX-ray3.80C1-318[»]
2R92X-ray3.80C1-318[»]
2R93X-ray4.00C1-318[»]
2VUMX-ray3.40C1-318[»]
2YU9X-ray3.40C1-318[»]
3CQZX-ray2.80C1-318[»]
3FKIX-ray3.88C1-318[»]
3GTGX-ray3.78C1-318[»]
3GTJX-ray3.42C1-318[»]
3GTKX-ray3.80C1-318[»]
3GTLX-ray3.38C1-318[»]
3GTMX-ray3.80C1-318[»]
3GTOX-ray4.00C1-318[»]
3GTPX-ray3.90C1-318[»]
3GTQX-ray3.80C1-318[»]
3H3VX-ray4.00D1-318[»]
3HOUX-ray3.20C/O1-318[»]
3HOVX-ray3.50C1-318[»]
3HOWX-ray3.60C2-318[»]
3HOXX-ray3.65C2-318[»]
3HOYX-ray3.40C2-318[»]
3HOZX-ray3.65C2-318[»]
3I4MX-ray3.70C1-318[»]
3I4NX-ray3.90C1-318[»]
3J0Kelectron microscopy36.00C1-268[»]
3J1Nelectron microscopy16.00C1-268[»]
3K1FX-ray4.30C1-318[»]
3K7AX-ray3.80C1-318[»]
3M3YX-ray3.18C1-318[»]
3M4OX-ray3.57C1-318[»]
3PO2X-ray3.30C1-318[»]
3PO3X-ray3.30C1-318[»]
3QT1X-ray4.30C1-318[»]
3RZDX-ray3.30C1-318[»]
3RZOX-ray3.00C1-318[»]
3S14X-ray2.85C1-318[»]
3S15X-ray3.30C1-318[»]
3S16X-ray3.24C1-318[»]
3S17X-ray3.20C1-318[»]
3S1MX-ray3.13C1-318[»]
3S1NX-ray3.10C1-318[»]
3S1QX-ray3.30C1-318[»]
3S1RX-ray3.20C1-318[»]
3S2DX-ray3.20C1-318[»]
3S2HX-ray3.30C1-318[»]
4A3BX-ray3.50C1-318[»]
4A3CX-ray3.50C1-318[»]
4A3DX-ray3.40C1-318[»]
4A3EX-ray3.40C1-318[»]
4A3FX-ray3.50C1-318[»]
4A3GX-ray3.50C1-318[»]
4A3IX-ray3.80C1-318[»]
4A3JX-ray3.70C1-318[»]
4A3KX-ray3.50C1-318[»]
4A3LX-ray3.50C1-318[»]
4A3MX-ray3.90C1-318[»]
4A93X-ray3.40C1-318[»]
4BBRX-ray3.40C1-318[»]
4BBSX-ray3.60C1-318[»]
4BXXX-ray3.28C1-318[»]
4BXZX-ray4.80C1-318[»]
4BY1X-ray3.60C1-318[»]
4BY7X-ray3.15C1-318[»]
4V1Melectron microscopy6.60C1-318[»]
4V1Nelectron microscopy7.80C1-318[»]
4V1Oelectron microscopy9.70C1-318[»]
4X67X-ray4.10C1-318[»]
4X6AX-ray3.96C1-318[»]
4Y52X-ray3.50C1-318[»]
4Y7NX-ray3.30C1-318[»]
5C3EX-ray3.70C1-318[»]
5C44X-ray3.95C1-318[»]
5C4AX-ray4.20C1-318[»]
5C4JX-ray4.00C1-318[»]
5C4XX-ray4.00C1-318[»]
5FMFelectron microscopy6.00C3-268[»]
5FYWelectron microscopy4.35C1-318[»]
5FZ5electron microscopy8.80C1-318[»]
5IP7X-ray3.52C3-268[»]
5IP9X-ray3.90C3-268[»]
5OT2X-ray3.20C1-318[»]
5SVAelectron microscopy15.30C1-318[»]
5U5QX-ray3.80C1-318[»]
5VVRelectron microscopy5.80C1-318[»]
5VVSelectron microscopy6.40C1-318[»]
6BLOX-ray3.40C1-318[»]
6BLPX-ray3.20C1-318[»]
6BM2X-ray3.40C1-318[»]
6BM4X-ray2.95C1-318[»]
6BQFX-ray3.35C1-318[»]
ProteinModelPortaliP16370
SMRiP16370
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP16370

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00640000091532
HOGENOMiHOG000230844
InParanoidiP16370
KOiK03011
OMAiMAIDWVQ
OrthoDBiEOG092C3EZ0

Family and domain databases

Gene3Di2.170.120.12, 1 hit
3.30.1360.10, 2 hits
InterProiView protein in InterPro
IPR001514 DNA-dir_RNA_pol_30-40kDasu_CS
IPR011262 DNA-dir_RNA_pol_insert
IPR011263 DNA-dir_RNA_pol_RpoA/D/Rpb3
IPR036603 RBP11-like
IPR036643 RNApol_insert_sf
PfamiView protein in Pfam
PF01000 RNA_pol_A_bac, 1 hit
PF01193 RNA_pol_L, 1 hit
SMARTiView protein in SMART
SM00662 RPOLD, 1 hit
SUPFAMiSSF55257 SSF55257, 1 hit
SSF56553 SSF56553, 1 hit
PROSITEiView protein in PROSITE
PS00446 RNA_POL_D_30KD, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P16370-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEEGPQVKI REASKDNVDF ILSNVDLAMA NSLRRVMIAE IPTLAIDSVE
60 70 80 90 100
VETNTTVLAD EFIAHRLGLI PLQSMDIEQL EYSRDCFCED HCDKCSVVLT
110 120 130 140 150
LQAFGESEST TNVYSKDLVI VSNLMGRNIG HPIIQDKEGN GVLICKLRKG
160 170 180 190 200
QELKLTCVAK KGIAKEHAKW GPAAAIEFEY DPWNKLKHTD YWYEQDSAKE
210 220 230 240 250
WPQSKNCEYE DPPNEGDPFD YKAQADTFYM NVESVGSIPV DQVVVRGIDT
260 270 280 290 300
LQKKVASILL ALTQMDQDKV NFASGDNNTA SNMLGSNEDV MMTGAEQDPY
310
SNASQMGNTG SGGYDNAW
Length:318
Mass (Da):35,298
Last modified:February 1, 1995 - v2
Checksum:i8E1D1E6BB7B51D89
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti175A → G in AAA34889 (PubMed:2685562).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti30A → D in mutant RPB3-1. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z46881 Genomic DNA Translation: CAA86971.1
M27496 Genomic DNA Translation: AAA34889.1
BK006942 Genomic DNA Translation: DAA08524.1
PIRiS49961
RefSeqiNP_012243.3, NM_001179371.3

Genome annotation databases

EnsemblFungiiYIL021W; YIL021W; YIL021W
GeneIDi854791
KEGGisce:YIL021W

Keywords - Coding sequence diversityi

Polymorphism

Similar proteinsi

Entry informationi

Entry nameiRPB3_YEAST
AccessioniPrimary (citable) accession number: P16370
Secondary accession number(s): D6VVQ8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: February 1, 1995
Last modified: May 23, 2018
This is version 189 of the entry and version 2 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 IX
    Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

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