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Protein

RNA polymerase II subunit B1 CTD phosphatase RTR1

Gene

RTR1

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

RNA polymerase II subunit B1 C-terminal domain (CTD) phosphatase that dephosphorylates 'Ser-5' of the CTD and regulates RNA polymerase II during the transition from 'Ser-5' to 'Ser-2' phosphorylation.2 Publications

Catalytic activityi

[a protein]-serine/threonine phosphate + H2O = [a protein]-serine/threonine + phosphate.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi73ZincPROSITE-ProRule annotation1
Metal bindingi78ZincPROSITE-ProRule annotation1
Metal bindingi112ZincPROSITE-ProRule annotation1
Metal bindingi116ZincPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri50 – 136RTR1-typePROSITE-ProRule annotationAdd BLAST87

GO - Molecular functioni

  • CTD phosphatase activity Source: SGD
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • dephosphorylation of RNA polymerase II C-terminal domain Source: SGD
  • transcription from RNA polymerase II promoter Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protein phosphatase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-30300-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase II subunit B1 CTD phosphatase RTR1 (EC:3.1.3.16)
Alternative name(s):
RNA polymerase II-associated protein 2 homolog RTR1
Regulator of transcription 1
Gene namesi
Name:RTR1
Ordered Locus Names:YER139C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YER139C.
SGDiS000000941. RTR1.

Subcellular locationi

  • Cytoplasm
  • Nucleus

  • Note: Shuttles constitutively between the cytoplasm and the nucleus.

GO - Cellular componenti

  • cytoplasm Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi73C → S: Loss of function. 1 Publication1
Mutagenesisi112C → S: Loss of function; when associated with S-116. 1 Publication1
Mutagenesisi116H → S: Loss of function; when associated with S-112. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002026531 – 226RNA polymerase II subunit B1 CTD phosphatase RTR1Add BLAST226

Proteomic databases

MaxQBiP40084.
PRIDEiP40084.

PTM databases

iPTMnetiP40084.

Interactioni

Subunit structurei

Interacts with RPO21.1 Publication

Protein-protein interaction databases

BioGridi36888. 84 interactors.
DIPiDIP-6690N.
IntActiP40084. 9 interactors.
MINTiMINT-649086.

Structurei

Secondary structure

1226
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 11Combined sources8
Helixi13 – 15Combined sources3
Helixi23 – 37Combined sources15
Beta strandi38 – 40Combined sources3
Beta strandi42 – 44Combined sources3
Helixi45 – 51Combined sources7
Helixi52 – 54Combined sources3
Helixi57 – 69Combined sources13
Helixi91 – 99Combined sources9
Beta strandi100 – 102Combined sources3
Helixi105 – 108Combined sources4
Beta strandi111 – 113Combined sources3
Helixi114 – 124Combined sources11
Helixi132 – 134Combined sources3
Turni136 – 139Combined sources4
Helixi146 – 152Combined sources7
Helixi158 – 165Combined sources8
Helixi168 – 175Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5C2YX-ray2.60A/B1-178[»]
ProteinModelPortaliP40084.
SMRiP40084.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RPAP2 family.Curated
Contains 1 RTR1-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri50 – 136RTR1-typePROSITE-ProRule annotationAdd BLAST87

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00530000069589.
HOGENOMiHOG000000844.
InParanoidiP40084.
KOiK20827.
OMAiHFRCSQF.
OrthoDBiEOG092C3XCU.

Family and domain databases

InterProiIPR007308. DUF408.
[Graphical view]
PfamiPF04181. RPAP2_Rtr1. 1 hit.
[Graphical view]
PROSITEiPS51479. ZF_RTR1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P40084-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATIEDIKET ALIPFQKHRQ LSMHEAEVIT LEIIGLLCDS ECKDEKTLKY
60 70 80 90 100
LGRFLTPDMY QDLVDERNLN KRCGYPLCGK SPERIRDPFS MNDTTKKFLL
110 120 130 140 150
ENNPYAYLSH YCSKFHFRCS QFYQVQLSDE ALFARTGVHL FEDPEQDKHD
160 170 180 190 200
IDFKVTLFEE LLREKASEED IKSLISGLKK LGLNPDSGTT EKDDTELEDD
210 220
LSKWLAQIKI VENDNPSILG DFTRED
Length:226
Mass (Da):26,240
Last modified:February 1, 1995 - v1
Checksum:iE234D9ADC18C3FCA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18917 Genomic DNA. Translation: AAB64666.1.
BK006939 Genomic DNA. Translation: DAA07800.1.
PIRiS50642.
RefSeqiNP_011066.3. NM_001179029.3.

Genome annotation databases

EnsemblFungiiYER139C; YER139C; YER139C.
GeneIDi856882.
KEGGisce:YER139C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18917 Genomic DNA. Translation: AAB64666.1.
BK006939 Genomic DNA. Translation: DAA07800.1.
PIRiS50642.
RefSeqiNP_011066.3. NM_001179029.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5C2YX-ray2.60A/B1-178[»]
ProteinModelPortaliP40084.
SMRiP40084.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36888. 84 interactors.
DIPiDIP-6690N.
IntActiP40084. 9 interactors.
MINTiMINT-649086.

PTM databases

iPTMnetiP40084.

Proteomic databases

MaxQBiP40084.
PRIDEiP40084.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYER139C; YER139C; YER139C.
GeneIDi856882.
KEGGisce:YER139C.

Organism-specific databases

EuPathDBiFungiDB:YER139C.
SGDiS000000941. RTR1.

Phylogenomic databases

GeneTreeiENSGT00530000069589.
HOGENOMiHOG000000844.
InParanoidiP40084.
KOiK20827.
OMAiHFRCSQF.
OrthoDBiEOG092C3XCU.

Enzyme and pathway databases

BioCyciYEAST:G3O-30300-MONOMER.

Miscellaneous databases

PROiP40084.

Family and domain databases

InterProiIPR007308. DUF408.
[Graphical view]
PfamiPF04181. RPAP2_Rtr1. 1 hit.
[Graphical view]
PROSITEiPS51479. ZF_RTR1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRTR1_YEAST
AccessioniPrimary (citable) accession number: P40084
Secondary accession number(s): D3DM46
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: November 30, 2016
This is version 121 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 5480 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 V
    Yeast (Saccharomyces cerevisiae) chromosome V: 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.