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Protein

DNA-directed RNA polymerase I subunit RPA12

Gene

RPA12

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. Proposed to contribute to the polymerase catalytic activity and form the polymerase active center together with the two largest subunits. Subunit RPA12 contributes a catalytic zinc ribbon that is required for RNA cleavage by Pol I. Involved in transcriptional termination.4 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri10 – 3324C4-typeAdd
BLAST
Zinc fingeri82 – 12241TFIIS-typePROSITE-ProRule annotation2 PublicationsAdd
BLAST

GO - Molecular functioni

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

GO - Biological processi

  • ribosome biogenesis Source: UniProtKB-KW
  • termination of RNA polymerase I transcription 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 - Biological processi

Ribosome biogenesis, Transcription

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-31696-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase I subunit RPA12
Alternative name(s):
A12
A12.2
DNA-directed RNA polymerase I 13.7 kDa polypeptide
Gene namesi
Name:RPA12
Synonyms:RRN4
Ordered Locus Names:YJR063W
ORF Names:J1747
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJR063W.
SGDiS000003824. RPA12.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

DNA-directed RNA polymerase, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi10 – 101C → S: Severe growth defect. 1 Publication
Mutagenesisi13 – 131C → S: No effect. 1 Publication
Mutagenesisi30 – 301C → S: Limited growth defect. 1 Publication
Mutagenesisi33 – 331C → S: No effect. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 125125DNA-directed RNA polymerase I subunit RPA12PRO_0000121465Add
BLAST

Proteomic databases

MaxQBiP32529.
PeptideAtlasiP32529.
PRIDEiP32529.

PTM databases

iPTMnetiP32529.

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. Interacts with RPA2/RPA135. Peripheral subunit that binds the catalytic zinc ion that is required for RNA cleavage. The heterodimer formed by RPA34 and RPA49 stabilizes subunit RPA12 and stimulates RPA12-dependent RNA cleavage. Involved in the recruitment of RPA49 to Pol I.5 Publications

Protein-protein interaction databases

BioGridi33820. 34 interactions.
DIPiDIP-236N.
IntActiP32529. 27 interactions.
MINTiMINT-472816.

Structurei

Secondary structure

1
125
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 93Combined sources
Beta strandi11 – 133Combined sources
Helixi20 – 223Combined sources
Beta strandi24 – 296Combined sources
Turni31 – 333Combined sources
Beta strandi36 – 394Combined sources
Beta strandi47 – 504Combined sources
Helixi53 – 553Combined sources
Helixi59 – 635Combined sources
Beta strandi65 – 673Combined sources
Beta strandi79 – 835Combined sources
Turni87 – 893Combined sources
Beta strandi92 – 998Combined sources
Beta strandi104 – 1063Combined sources
Beta strandi109 – 1146Combined sources
Turni115 – 1173Combined sources
Beta strandi120 – 1234Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4C2MX-ray2.80I/X1-125[»]
4C3HX-ray3.27I1-125[»]
4C3IX-ray3.0I1-125[»]
4C3JX-ray3.35I1-125[»]
4YM7X-ray5.50AI/BI/CI/DI/EI/FI1-125[»]
ProteinModelPortaliP32529.
SMRiP32529. Positions 2-125.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 6969Necessary and sufficient for recruitment into Pol IAdd
BLAST
Regioni1 – 6060Interaction with RPA2Add
BLAST
Regioni79 – 12547Required for RNA cleavage, but not essential for elongation activityAdd
BLAST

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri10 – 3324C4-typeAdd
BLAST
Zinc fingeri82 – 12241TFIIS-typePROSITE-ProRule annotation2 PublicationsAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000008126.
HOGENOMiHOG000228133.
InParanoidiP32529.
KOiK03000.
OMAiHGWRVNN.
OrthoDBiEOG7N37RR.

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.

P32529-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVVGSLIFC LDCGDLLENP NAVLGSNVEC SQCKAIYPKS QFSNLKVVTT
60 70 80 90 100
TADDAFPSSL RAKKSVVKTS LKKNELKDGA TIKEKCPQCG NEEMNYHTLQ
110 120
LRSADEGATV FYTCTSCGYK FRTNN
Length:125
Mass (Da):13,661
Last modified:October 1, 1993 - v1
Checksum:iD79372070819987C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L00708 Genomic DNA. Translation: AAA34992.1.
L35564 Genomic DNA. Translation: AAB59319.1.
Z49563 Genomic DNA. Translation: CAA89591.1.
L47993 Genomic DNA. Translation: AAB39289.1.
AY558313 Genomic DNA. Translation: AAS56639.1.
BK006943 Genomic DNA. Translation: DAA08850.1.
PIRiA48107.
RefSeqiNP_012597.1. NM_001181721.1.

Genome annotation databases

EnsemblFungiiYJR063W; YJR063W; YJR063W.
GeneIDi853526.
KEGGisce:YJR063W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L00708 Genomic DNA. Translation: AAA34992.1.
L35564 Genomic DNA. Translation: AAB59319.1.
Z49563 Genomic DNA. Translation: CAA89591.1.
L47993 Genomic DNA. Translation: AAB39289.1.
AY558313 Genomic DNA. Translation: AAS56639.1.
BK006943 Genomic DNA. Translation: DAA08850.1.
PIRiA48107.
RefSeqiNP_012597.1. NM_001181721.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4C2MX-ray2.80I/X1-125[»]
4C3HX-ray3.27I1-125[»]
4C3IX-ray3.0I1-125[»]
4C3JX-ray3.35I1-125[»]
4YM7X-ray5.50AI/BI/CI/DI/EI/FI1-125[»]
ProteinModelPortaliP32529.
SMRiP32529. Positions 2-125.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33820. 34 interactions.
DIPiDIP-236N.
IntActiP32529. 27 interactions.
MINTiMINT-472816.

PTM databases

iPTMnetiP32529.

Proteomic databases

MaxQBiP32529.
PeptideAtlasiP32529.
PRIDEiP32529.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYJR063W; YJR063W; YJR063W.
GeneIDi853526.
KEGGisce:YJR063W.

Organism-specific databases

EuPathDBiFungiDB:YJR063W.
SGDiS000003824. RPA12.

Phylogenomic databases

GeneTreeiENSGT00390000008126.
HOGENOMiHOG000228133.
InParanoidiP32529.
KOiK03000.
OMAiHGWRVNN.
OrthoDBiEOG7N37RR.

Enzyme and pathway databases

BioCyciYEAST:G3O-31696-MONOMER.

Miscellaneous databases

PROiP32529.

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...

Publicationsi

« Hide 'large scale' publications
  1. "Gene RRN4 in Saccharomyces cerevisiae encodes the A12.2 subunit of RNA polymerase I and is essential only at high temperatures."
    Nogi Y., Yano R., Dodd J., Carles C., Nomura M.
    Mol. Cell. Biol. 13:114-122(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
  2. "Analysis of a 62 kb DNA sequence of chromosome X reveals 36 open reading frames and a gene cluster with a counterpart on chromosome XI."
    Huang M.-E., Manus V., Chuat J.-C., Galibert F.
    Yeast 12:869-875(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
    Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
    , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
    EMBO J. 15:2031-2049(1996) [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. "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: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. "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 POLYMERASE I COMPLEX.
  8. "Rpa12p, a conserved RNA polymerase I subunit with two functional domains."
    Van Mullem V., Landrieux E., Vandenhaute J., Thuriaux P.
    Mol. Microbiol. 43:1105-1113(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE RNA POL I COMPLEX, SUBCELLULAR LOCATION, INTERACTION WITH RPA2, MUTAGENESIS OF CYS-10; CYS-13; CYS-30 AND CYS-33.
  9. "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.
  10. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  11. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  12. "Transcriptional termination by RNA polymerase I requires the small subunit Rpa12p."
    Prescott E.M., Osheim Y.N., Jones H.S., Alen C.M., Roan J.G., Reeder R.H., Beyer A.L., Proudfoot N.J.
    Proc. Natl. Acad. Sci. U.S.A. 101:6068-6073(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  13. Cited for: STRUCTURE BY ELECTRON MICROSCOPY (12.00 ANGSTROMS) OF THE POL I COMPLEX, FUNCTION IN RNA CLEAVAGE, REGION, SUBUNIT.
  14. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE POL I COMPLEX IN COMPLEX WITH ZINC IONS, FUNCTION, ZINC-BINDING, SUBUNIT, ZINC FINGER DOMAIN.
  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 IN COMPLEX WITH ZINC IONS, FUNCTION, ZINC-BINDING, SUBUNIT, ZINC FINGER DOMAIN.

Entry informationi

Entry nameiRPA12_YEAST
AccessioniPrimary (citable) accession number: P32529
Secondary accession number(s): D6VWN4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: June 8, 2016
This is version 149 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 8450 molecules/cell in log phase SD medium.1 Publication

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 X
    Yeast (Saccharomyces cerevisiae) chromosome X: 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.