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Protein

DNA-directed RNA polymerase I subunit RPA49

Gene

RPA49

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. Component of RNA polymerase I (Pol I) which synthesizes ribosomal RNA precursors. Besides, RNA polymerase I has intrinsic RNA cleavage activity. The heterodimer formed by RPA34 and RPA49 stimulates transcript elongation by Pol I. Subunit RPA49 can bind both single-stranded and double-stranded DNA.4 Publications

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • RNA polymerase I activity Source: UniProtKB

GO - Biological processi

  • ribosome biogenesis Source: UniProtKB-KW
  • transcription elongation from RNA polymerase I promoter Source: SGD
  • transcription from RNA polymerase I promoter Source: UniProtKB
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Ribosome biogenesis, Transcription

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33245-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase I subunit RPA49
Short name:
A49
Alternative name(s):
DNA-directed RNA polymerase I 49 kDa polypeptide
Gene namesi
Name:RPA49
Synonyms:RRN13
Ordered Locus Names:YNL248C
ORF Names:N0880
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIV

Organism-specific databases

EuPathDBiFungiDB:YNL248C.
SGDiS000005192. RPA49.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi325 – 3262ED → AA: No effect on DNA binding. 1 Publication
Mutagenesisi356 – 3561K → A: Loss of DNA binding; when associated with A-358. 1 Publication
Mutagenesisi358 – 3581S → A: Loss of DNA binding; when associated with A-356. 1 Publication
Mutagenesisi359 – 3591K → A: Loss of DNA binding. 1 Publication
Mutagenesisi365 – 3651R → A: Loss of DNA binding. 1 Publication
Mutagenesisi393 – 3931K → A: Loss of DNA binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 415415DNA-directed RNA polymerase I subunit RPA49PRO_0000073955Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei34 – 341PhosphoserineCombined sources
Modified residuei151 – 1511PhosphoserineCombined sources

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ01080.

PTM databases

iPTMnetiQ01080.

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. 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. Forms a TFIIF-like heterodimer with RPA34; the heterodimer formed by RPA34 and RPA49 can be dissociated from the Pol I core giving rise to a 12 subunit form A* of Pol I (formerly called pol A) that shows impaired transcript elongation activity and increased sensitivity to alpha-amanitin. The heterodimer formed by RPA34 and RPA49 stabilizes subunit RPA12 and stimulates RPA12-dependent RNA cleavage.6 Publications

Protein-protein interaction databases

BioGridi35591. 181 interactions.
DIPiDIP-6577N.
IntActiQ01080. 15 interactions.
MINTiMINT-630569.

Structurei

Secondary structure

1
415
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi11 – 166Combined sources
Beta strandi22 – 254Combined sources
Beta strandi37 – 426Combined sources
Beta strandi51 – 566Combined sources
Beta strandi58 – 658Combined sources
Helixi70 – 723Combined sources
Beta strandi74 – 829Combined sources
Turni83 – 864Combined sources
Beta strandi87 – 926Combined sources
Beta strandi95 – 1028Combined sources
Helixi103 – 1064Combined sources
Helixi173 – 18412Combined sources
Helixi198 – 2003Combined sources
Helixi204 – 2074Combined sources
Helixi210 – 2134Combined sources
Helixi219 – 2235Combined sources
Helixi227 – 2326Combined sources
Helixi242 – 2476Combined sources
Helixi253 – 2553Combined sources
Helixi256 – 27318Combined sources
Turni274 – 2763Combined sources
Helixi280 – 2845Combined sources
Helixi292 – 30211Combined sources
Beta strandi303 – 3053Combined sources
Helixi309 – 3146Combined sources
Beta strandi317 – 3193Combined sources
Helixi322 – 33918Combined sources
Turni340 – 3423Combined sources
Beta strandi343 – 3453Combined sources
Helixi346 – 3538Combined sources
Helixi357 – 36610Combined sources
Beta strandi370 – 3734Combined sources
Helixi376 – 3827Combined sources
Helixi386 – 3916Combined sources
Beta strandi392 – 3965Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3NFHX-ray2.17A/B154-399[»]
3NFIX-ray1.90A/B/C/D/E171-403[»]
4C2MX-ray2.802/M1-415[»]
4C3HX-ray3.27M1-415[»]
4C3IX-ray3.0M1-415[»]
4C3JX-ray3.35M1-415[»]
4YM7X-ray5.50AM/BM/CM/DM/EM/FM1-415[»]
ProteinModelPortaliQ01080.
SMRiQ01080. Positions 8-115, 184-403.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ01080.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni322 – 41594Interaction with DNAAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000018004.
HOGENOMiHOG000057118.
InParanoidiQ01080.
KOiK03005.
OMAiTHMFALC.
OrthoDBiEOG7P2Z2M.

Family and domain databases

InterProiIPR009668. RNA_pol-assoc_fac_A49-like.
[Graphical view]
PfamiPF06870. RNA_pol_I_A49. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q01080-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVKRSVSEI EIESVQDQPS VAVGSFFKGF RAPSDTTFDL YKKKKSEKDE
60 70 80 90 100
FVLHGENERL EYEGYTDSSS QASNQYVVGL FNPEKKSIQL YKAPVLVSKV
110 120 130 140 150
VSKSSKNLRG PKIKSKSDTR PSALRNALGE AFGTKKAKKA IADLERNRID
160 170 180 190 200
SDKLTDSAID IVDSVRTASK DLPTRAQLDE ITSNDRPTPL ANIDATDVEQ
210 220 230 240 250
IYPIESIIPK KELQFIRVSS ILKEADKEKK LELFPYQNNS KYVAKKLDSL
260 270 280 290 300
TQPSQMTKLQ LLYYLSLLLG VYENRRVNNK TKLLERLNSP PEILVDGILS
310 320 330 340 350
RFTVIKPGQF GRSKDRSYFI DPQNEDKILC YILAIIMHLD NFIVEITPLA
360 370 380 390 400
HELNLKPSKV VSLFRVLGAI VKGATVAQAE AFGIPKSTAA SYKIATMKVP
410
FKLPEMTRRG RGPRR
Length:415
Mass (Da):46,651
Last modified:October 1, 1996 - v2
Checksum:i3D9BF05440D26021
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti66 – 661T → P in AAA34380 (PubMed:1409638).Curated
Sequence conflicti157 – 1571S → C in AAA34380 (PubMed:1409638).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M96600 Genomic DNA. Translation: AAA34380.1.
X96722 Genomic DNA. Translation: CAA65496.1.
Z71524 Genomic DNA. Translation: CAA96155.1.
AY558027 Genomic DNA. Translation: AAS56353.1.
BK006947 Genomic DNA. Translation: DAA10311.1.
PIRiS63221.
RefSeqiNP_014151.1. NM_001183086.1.

Genome annotation databases

EnsemblFungiiYNL248C; YNL248C; YNL248C.
GeneIDi855473.
KEGGisce:YNL248C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M96600 Genomic DNA. Translation: AAA34380.1.
X96722 Genomic DNA. Translation: CAA65496.1.
Z71524 Genomic DNA. Translation: CAA96155.1.
AY558027 Genomic DNA. Translation: AAS56353.1.
BK006947 Genomic DNA. Translation: DAA10311.1.
PIRiS63221.
RefSeqiNP_014151.1. NM_001183086.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3NFHX-ray2.17A/B154-399[»]
3NFIX-ray1.90A/B/C/D/E171-403[»]
4C2MX-ray2.802/M1-415[»]
4C3HX-ray3.27M1-415[»]
4C3IX-ray3.0M1-415[»]
4C3JX-ray3.35M1-415[»]
4YM7X-ray5.50AM/BM/CM/DM/EM/FM1-415[»]
ProteinModelPortaliQ01080.
SMRiQ01080. Positions 8-115, 184-403.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35591. 181 interactions.
DIPiDIP-6577N.
IntActiQ01080. 15 interactions.
MINTiMINT-630569.

PTM databases

iPTMnetiQ01080.

Proteomic databases

MaxQBiQ01080.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYNL248C; YNL248C; YNL248C.
GeneIDi855473.
KEGGisce:YNL248C.

Organism-specific databases

EuPathDBiFungiDB:YNL248C.
SGDiS000005192. RPA49.

Phylogenomic databases

GeneTreeiENSGT00390000018004.
HOGENOMiHOG000057118.
InParanoidiQ01080.
KOiK03005.
OMAiTHMFALC.
OrthoDBiEOG7P2Z2M.

Enzyme and pathway databases

BioCyciYEAST:G3O-33245-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ01080.
PROiQ01080.

Family and domain databases

InterProiIPR009668. RNA_pol-assoc_fac_A49-like.
[Graphical view]
PfamiPF06870. RNA_pol_I_A49. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization and mutagenesis of the gene encoding the A49 subunit of RNA polymerase A in Saccharomyces cerevisiae."
    Liljelund P., Mariotte S., Buhler J.-M., Sentenac A.
    Proc. Natl. Acad. Sci. U.S.A. 89:9302-9305(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: CMY214.
  2. "Sequence analysis of the 33 kb long region between ORC5 and SUI1 from the left arm of chromosome XIV from Saccharomyces cerevisiae."
    Sen-Gupta M., Gueldener U., Beinhauer J.D., Fiedler T.A., Hegemann J.H.
    Yeast 13:849-860(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 96604 / S288c / FY1679.
  3. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
    Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J.
    , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
    Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  4. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  6. "Differential roles of phosphorylation in the formation of transcriptional active RNA polymerase I."
    Fath S., Milkereit P., Peyroche G., Riva M., Carles C., Tschochner H.
    Proc. Natl. Acad. Sci. U.S.A. 98:14334-14339(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE RNA POL I COMPLEX.
  7. "A multidimensional chromatography technology for in-depth phosphoproteome analysis."
    Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
    Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-34, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
    Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
    Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-151, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "Localization of the yeast RNA polymerase I-specific subunits."
    Bischler N., Brino L., Carles C., Riva M., Tschochner H., Mallouh V., Schultz P.
    EMBO J. 21:4136-4144(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: ELECTRON MICROSCOPY OF THE RNA POL I COMPLEX.
  10. "The A14-A43 heterodimer subunit in yeast RNA pol I and their relationship to Rpb4-Rpb7 pol II subunits."
    Peyroche G., Levillain E., Siaut M., Callebaut I., Schultz P., Sentenac A., Riva M., Carles C.
    Proc. Natl. Acad. Sci. U.S.A. 99:14670-14675(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE RNA POL I COMPLEX.
  11. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  12. Cited for: STRUCTURE BY ELECTRON MICROSCOPY (12.00 ANGSTROMS) OF THE POL I COMPLEX, FUNCTION, SUBUNIT.
  13. "RNA polymerase I contains a TFIIF-related DNA-binding subcomplex."
    Geiger S.R., Lorenzen K., Schreieck A., Hanecker P., Kostrewa D., Heck A.J., Cramer P.
    Mol. Cell 39:583-594(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 171-403, FUNCTION, INTERACTION WITH RPA34, DNA-BINDING, MUTAGENESIS OF 325-ASP-GLU-326; LYS-356; SER-358; LYS-359; ARG-365 AND LYS-393, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT.
  14. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE POL I COMPLEX, FUNCTION, SUBUNIT.
  15. "RNA polymerase I structure and transcription regulation."
    Engel C., Sainsbury S., Cheung A.C., Kostrewa D., Cramer P.
    Nature 502:650-655(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE POL I COMPLEX, FUNCTION, SUBUNIT.

Entry informationi

Entry nameiRPA49_YEAST
AccessioniPrimary (citable) accession number: Q01080
Secondary accession number(s): D6W0U5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: October 1, 1996
Last modified: July 6, 2016
This is version 137 of the entry and version 2 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. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XIV
    Yeast (Saccharomyces cerevisiae) chromosome XIV: 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.