P40084 (RTR1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	RTR1
Ordered Locus Names:	YER139C

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	226 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.5 Ref.6
Catalytic activity	A phosphoprotein + H2O = a protein + phosphate.
Subunit structure	Interacts with RPO21. Ref.5
Subcellular location	Cytoplasm. Nucleus. Note: Shuttles constitutively between the cytoplasm and the nucleus. Ref.3 Ref.5 Ref.6
Miscellaneous	Present with 5480 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the RPAP2 family. Contains 1 RTR1-type zinc finger.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Hydrolase Protein phosphatase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	dephosphorylation of RNA polymerase II C-terminal domain Inferred from mutant phenotype Ref.6. Source: SGD transcription from RNA polymerase II promoter Inferred from mutant phenotype Ref.5. Source: SGD
Cellular_component	cytoplasm Inferred from direct assay Ref.3Ref.5. Source: SGD nucleus Inferred from direct assay Ref.5. Source: SGD
Molecular_function	CTD phosphatase activity Inferred from direct assay Ref.6. Source: SGD metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 226	226	RNA polymerase II subunit B1 CTD phosphatase RTR1		PRO_0000202653
Regions
	Zinc finger	50 – 136	87	RTR1-type
Experimental info
	Mutagenesis	73	1	C → S: Loss of function. Ref.5
	Mutagenesis	112	1	C → S: Loss of function; when associated with S-116. Ref.5
	Mutagenesis	116	1	H → S: Loss of function; when associated with S-112. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	P40084 [UniParc]. Last modified February 1, 1995. Version 1. Checksum: E234D9ADC18C3FCA	FASTA	226	26,240
	10 20 30 40 50 60 MATIEDIKET ALIPFQKHRQ LSMHEAEVIT LEIIGLLCDS ECKDEKTLKY LGRFLTPDMY 70 80 90 100 110 120 QDLVDERNLN KRCGYPLCGK SPERIRDPFS MNDTTKKFLL ENNPYAYLSH YCSKFHFRCS 130 140 150 160 170 180 QFYQVQLSDE ALFARTGVHL FEDPEQDKHD IDFKVTLFEE LLREKASEED IKSLISGLKK 190 200 210 220 LGLNPDSGTT EKDDTELEDD LSKWLAQIKI VENDNPSILG DFTRED

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome V." Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E., Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S., Hyman R.W. , Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D., Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X., Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y., Botstein D., Davis R.W. Nature 387:78-81(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[2]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[3]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[4]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[5]	"Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteins." Gibney P.A., Fries T., Bailer S.M., Morano K.A. Eukaryot. Cell 7:938-948(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, ZINC-FINGER, MUTAGENESIS OF CYS-73; CYS-112 AND HIS-116, INTERACTION WITH RPO21.
[6]	"Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the transition from serine 5 to serine 2 phosphorylation." Mosley A.L., Pattenden S.G., Carey M., Venkatesh S., Gilmore J.M., Florens L., Workman J.L., Washburn M.P. Mol. Cell 34:168-178(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U18917 Genomic DNA. Translation: AAB64666.1. BK006939 Genomic DNA. Translation: DAA07800.1.
PIR	S50642.
RefSeq	NP_011066.3. NM_001179029.3.
3D structure databases
ProteinModelPortal	P40084.
SMR	P40084. Positions 1-146.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-6690N.
IntAct	P40084. 8 interactions.
MINT	MINT-649086.
STRING	4932.YER139C.
Proteomic databases
PaxDb	P40084.
PeptideAtlas	P40084.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YER139C; YER139C; YER139C.
GeneID	856882.
KEGG	sce:YER139C. sce:YER143W.
Organism-specific databases
CYGD	YER139c.
SGD	S000000941. RTR1.
Phylogenomic databases
eggNOG	NOG315830.
GeneTree	ENSGT00530000069589.
HOGENOM	HOG000000844.
KO	K11885.
OMA	HFRCSQF.
OrthoDB	EOG4SFDGB.
Gene expression databases
Genevestigator	P40084.
GermOnline	YER139C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR007308. DUF408. [Graphical view]
Pfam	PF04181. RPAP2_Rtr1. 1 hit. [Graphical view]
PROSITE	PS51479. ZF_RTR1. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	983269.

Entry information

Entry name

RTR1_YEAST

Accession

Primary (citable) accession number: P40084
Secondary accession number(s): D3DM46

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	February 1, 1995
Last modified:	May 1, 2013
This is version 96 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program