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Protein

DNA-directed RNA polymerases I and III subunit RPAC1

Gene

RPC40

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA-dependent RNA polymerases catalyze the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I (Pol I) and III (Pol III) which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPC40 is part of the polymerase core and may function as a clamp element that moves to open and close the cleft (PubMed:18160037, PubMed:24153182, PubMed:24153184). Plays an important role in targeting retrotransposons Ty integration upstream of pol III-transcribed genes such as tRNA genes, allowing Ty1, Ty2 and Ty4 to proliferate and yet minimizing genetic damage (PubMed:25931562).1 Publication4 Publications

GO - Molecular functioni

  • DNA binding Source: InterPro
  • RNA polymerase I activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Ribosome biogenesis, Transcription

Enzyme and pathway databases

BioCyciYEAST:G3O-34250-MONOMER.
ReactomeiR-SCE-73762. RNA Polymerase I Transcription Initiation.
R-SCE-73780. RNA Polymerase III Chain Elongation.
R-SCE-73980. RNA Polymerase III Transcription Termination.
R-SCE-749476. RNA Polymerase III Abortive And Retractive Initiation.
R-SCE-76061. RNA Polymerase III Transcription Initiation From Type 1 Promoter.
R-SCE-76066. RNA Polymerase III Transcription Initiation From Type 2 Promoter.
R-SCE-76071. RNA Polymerase III Transcription Initiation From Type 3 Promoter.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerases I and III subunit RPAC1Curated
Short name:
RNA polymerases I and III subunit AC1Curated
Alternative name(s):
C37
DNA-directed RNA polymerases I and III 40 kDa polypeptide1 Publication
Short name:
AC401 Publication
Short name:
C40Curated
Gene namesi
Name:RPC401 Publication
Synonyms:RPC5Imported
Ordered Locus Names:YPR110CImported
ORF Names:P8283.18
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPR110C.
SGDiS000006314. RPC40.

Subcellular locationi

GO - Cellular componenti

  • DNA-directed RNA polymerase I complex Source: UniProtKB
  • DNA-directed RNA polymerase III complex Source: SGD
  • nucleoplasm Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001327422 – 335DNA-directed RNA polymerases I and III subunit RPAC1Add BLAST334

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei17PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiP07703.
PRIDEiP07703.

PTM databases

iPTMnetiP07703.

Interactioni

Subunit structurei

Component of the RNA polymerase I (Pol I) complex consisting of 14 subunits: RPA135, RPA190, RPC40, RPA14, RPB5, RPO26, RPA43, RPB8, RPA12, RPB10, RPC19, RPC10, RPA49 and RPA34 (PubMed:8516295, PubMed:11717393, PubMed:12407181, PubMed:18160037, PubMed:24153184, PubMed:24153182). The complex is composed of a horseshoe-shaped core containing ten subunits (RPA135, RPA190, RPB5, RPO26, RPB8, RPB10, RPC10, RPA12, RPC19 and RPC40) where RPA135 and RPA190 form the DNA-binding cleft. Outside of the core, RPA14 and RPA43 form the stalk that mediates interactions with transcription initiation factors and newly synthesized RNA. Component of the RNA polymerase III (Pol III) complex consisting of at least 17 subunits (PubMed:8516295, PubMed:10384303, PubMed:10393904). Interacts with the RPC19/RPAC2 (PubMed:8516295) and RPC53/RPC4 (PubMed:10393904). Interacts with retrotransposons Ty integrase, targeting Ty1, Ty2 and Ty4 integration upstream of pol III-transcribed genes (PubMed:25931562).1 Publication8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
RPA190P109645EBI-15831,EBI-15730
RPC19P280003EBI-15831,EBI-15846

Protein-protein interaction databases

BioGridi36277. 188 interactors.
DIPiDIP-17N.
IntActiP07703. 52 interactors.
MINTiMINT-395916.

Structurei

Secondary structure

1335
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi33 – 39Combined sources7
Beta strandi41 – 46Combined sources6
Beta strandi49 – 58Combined sources10
Helixi61 – 73Combined sources13
Beta strandi77 – 88Combined sources12
Beta strandi90 – 92Combined sources3
Helixi94 – 103Combined sources10
Helixi110 – 112Combined sources3
Beta strandi118 – 120Combined sources3
Helixi122 – 125Combined sources4
Turni128 – 130Combined sources3
Beta strandi132 – 139Combined sources8
Helixi153 – 156Combined sources4
Beta strandi157 – 159Combined sources3
Beta strandi161 – 163Combined sources3
Helixi164 – 166Combined sources3
Beta strandi168 – 170Combined sources3
Helixi175 – 178Combined sources4
Turni179 – 181Combined sources3
Beta strandi185 – 188Combined sources4
Beta strandi192 – 195Combined sources4
Beta strandi201 – 211Combined sources11
Turni213 – 215Combined sources3
Helixi217 – 219Combined sources3
Beta strandi222 – 237Combined sources16
Helixi242 – 248Combined sources7
Turni253 – 255Combined sources3
Beta strandi256 – 258Combined sources3
Turni260 – 262Combined sources3
Beta strandi264 – 268Combined sources5
Helixi270 – 272Combined sources3
Helixi278 – 281Combined sources4
Helixi283 – 286Combined sources4
Beta strandi289 – 304Combined sources16
Beta strandi306 – 308Combined sources3
Helixi310 – 329Combined sources20

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4C2MX-ray2.80C/R1-335[»]
4C3HX-ray3.27C1-335[»]
4C3IX-ray3.0C1-335[»]
4C3JX-ray3.35C1-335[»]
4YM7X-ray5.50AC/BC/CC/DC/EC/FC1-335[»]
5FJ8electron microscopy3.90C1-335[»]
5FJ9electron microscopy4.60C1-335[»]
5FJAelectron microscopy4.65C1-335[»]
5G5Lelectron microscopy4.80C1-335[»]
ProteinModelPortaliP07703.
SMRiP07703.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00550000075060.
HOGENOMiHOG000230845.
InParanoidiP07703.
KOiK03027.
OMAiECLRHPE.
OrthoDBiEOG092C3EZ0.

Family and domain databases

CDDicd07032. RNAP_I_II_AC40. 1 hit.
Gene3Di2.170.120.12. 1 hit.
InterProiIPR001514. DNA-dir_RNA_pol_30-40kDasu_CS.
IPR011262. DNA-dir_RNA_pol_insert.
IPR011263. DNA-dir_RNA_pol_RpoA/D/Rpb3.
IPR009025. RBP11-like_dimer.
IPR033901. RNAPI/II_AC40.
[Graphical view]
PfamiPF01000. RNA_pol_A_bac. 1 hit.
PF01193. RNA_pol_L. 1 hit.
[Graphical view]
SMARTiSM00662. RPOLD. 1 hit.
[Graphical view]
SUPFAMiSSF55257. SSF55257. 2 hits.
SSF56553. SSF56553. 1 hit.
PROSITEiPS00446. RNA_POL_D_30KD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P07703-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSNIVGIEYN RVTNTTSTDF PGFSKDAENE WNVEKFKKDF EVNISSLDAR
60 70 80 90 100
EANFDLINID TSIANAFRRI MISEVPSVAA EYVYFFNNTS VIQDEVLAHR
110 120 130 140 150
IGLVPLKVDP DMLTWVDSNL PDDEKFTDEN TIVLSLNVKC TRNPDAPKGS
160 170 180 190 200
TDPKELYNNA HVYARDLKFE PQGRQSTTFA DCPVVPADPD ILLAKLRPGQ
210 220 230 240 250
EISLKAHCIL GIGGDHAKFS PVSTASYRLL PQINILQPIK GESARRFQKC
260 270 280 290 300
FPPGVIGIDE GSDEAYVKDA RKDTVSREVL RYEEFADKVK LGRVRNHFIF
310 320 330
NVESAGAMTP EEIFFKSVRI LKNKAEYLKN CPITQ
Length:335
Mass (Da):37,687
Last modified:April 1, 1988 - v1
Checksum:i76A5D6784403E990
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15499 Genomic DNA. Translation: AAA34999.1.
U32445 Genomic DNA. Translation: AAB68080.1.
BK006949 Genomic DNA. Translation: DAA11525.1.
PIRiA25968.
RefSeqiNP_015435.1. NM_001184207.1.

Genome annotation databases

EnsemblFungiiYPR110C; YPR110C; YPR110C.
GeneIDi856226.
KEGGisce:YPR110C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15499 Genomic DNA. Translation: AAA34999.1.
U32445 Genomic DNA. Translation: AAB68080.1.
BK006949 Genomic DNA. Translation: DAA11525.1.
PIRiA25968.
RefSeqiNP_015435.1. NM_001184207.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4C2MX-ray2.80C/R1-335[»]
4C3HX-ray3.27C1-335[»]
4C3IX-ray3.0C1-335[»]
4C3JX-ray3.35C1-335[»]
4YM7X-ray5.50AC/BC/CC/DC/EC/FC1-335[»]
5FJ8electron microscopy3.90C1-335[»]
5FJ9electron microscopy4.60C1-335[»]
5FJAelectron microscopy4.65C1-335[»]
5G5Lelectron microscopy4.80C1-335[»]
ProteinModelPortaliP07703.
SMRiP07703.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36277. 188 interactors.
DIPiDIP-17N.
IntActiP07703. 52 interactors.
MINTiMINT-395916.

PTM databases

iPTMnetiP07703.

Proteomic databases

MaxQBiP07703.
PRIDEiP07703.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPR110C; YPR110C; YPR110C.
GeneIDi856226.
KEGGisce:YPR110C.

Organism-specific databases

EuPathDBiFungiDB:YPR110C.
SGDiS000006314. RPC40.

Phylogenomic databases

GeneTreeiENSGT00550000075060.
HOGENOMiHOG000230845.
InParanoidiP07703.
KOiK03027.
OMAiECLRHPE.
OrthoDBiEOG092C3EZ0.

Enzyme and pathway databases

BioCyciYEAST:G3O-34250-MONOMER.
ReactomeiR-SCE-73762. RNA Polymerase I Transcription Initiation.
R-SCE-73780. RNA Polymerase III Chain Elongation.
R-SCE-73980. RNA Polymerase III Transcription Termination.
R-SCE-749476. RNA Polymerase III Abortive And Retractive Initiation.
R-SCE-76061. RNA Polymerase III Transcription Initiation From Type 1 Promoter.
R-SCE-76066. RNA Polymerase III Transcription Initiation From Type 2 Promoter.
R-SCE-76071. RNA Polymerase III Transcription Initiation From Type 3 Promoter.

Miscellaneous databases

PROiP07703.

Family and domain databases

CDDicd07032. RNAP_I_II_AC40. 1 hit.
Gene3Di2.170.120.12. 1 hit.
InterProiIPR001514. DNA-dir_RNA_pol_30-40kDasu_CS.
IPR011262. DNA-dir_RNA_pol_insert.
IPR011263. DNA-dir_RNA_pol_RpoA/D/Rpb3.
IPR009025. RBP11-like_dimer.
IPR033901. RNAPI/II_AC40.
[Graphical view]
PfamiPF01000. RNA_pol_A_bac. 1 hit.
PF01193. RNA_pol_L. 1 hit.
[Graphical view]
SMARTiSM00662. RPOLD. 1 hit.
[Graphical view]
SUPFAMiSSF55257. SSF55257. 2 hits.
SSF56553. SSF56553. 1 hit.
PROSITEiPS00446. RNA_POL_D_30KD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPAC1_YEAST
AccessioniPrimary (citable) accession number: P07703
Secondary accession number(s): D6W4A9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: April 1, 1988
Last modified: November 30, 2016
This is version 170 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 13000 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, 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 XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

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.