ID   RTR1_YEAST              Reviewed;         226 AA.
AC   P40084; D3DM46;
DT   01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1995, sequence version 1.
DT   27-MAR-2024, entry version 161.
DE   RecName: Full=RNA polymerase II subunit B1 CTD phosphatase RTR1;
DE            EC=3.1.3.16;
DE   AltName: Full=RNA polymerase II-associated protein 2 homolog RTR1;
DE   AltName: Full=Regulator of transcription 1;
GN   Name=RTR1; OrderedLocusNames=YER139C;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169868;
RA   Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA   Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA   Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA   Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA   Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA   Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA   Botstein D., Davis R.W.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL   Nature 387:78-81(1997).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [3]
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=14562095; DOI=10.1038/nature02026;
RA   Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA   Weissman J.S., O'Shea E.K.;
RT   "Global analysis of protein localization in budding yeast.";
RL   Nature 425:686-691(2003).
RN   [4]
RP   LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX   PubMed=14562106; DOI=10.1038/nature02046;
RA   Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA   O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
RN   [5]
RP   FUNCTION, SUBCELLULAR LOCATION, ZINC-FINGER, MUTAGENESIS OF CYS-73; CYS-112
RP   AND HIS-116, AND INTERACTION WITH RPO21.
RX   PubMed=18408053; DOI=10.1128/ec.00042-08;
RA   Gibney P.A., Fries T., Bailer S.M., Morano K.A.;
RT   "Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA
RT   polymerase II-binding proteins.";
RL   Eukaryot. Cell 7:938-948(2008).
RN   [6]
RP   FUNCTION, AND SUBCELLULAR LOCATION.
RX   PubMed=19394294; DOI=10.1016/j.molcel.2009.02.025;
RA   Mosley A.L., Pattenden S.G., Carey M., Venkatesh S., Gilmore J.M.,
RA   Florens L., Workman J.L., Washburn M.P.;
RT   "Rtr1 is a CTD phosphatase that regulates RNA polymerase II during the
RT   transition from serine 5 to serine 2 phosphorylation.";
RL   Mol. Cell 34:168-178(2009).
CC   -!- FUNCTION: RNA polymerase II subunit B1 C-terminal domain (CTD)
CC       phosphatase that dephosphorylates 'Ser-5' of the CTD and regulates RNA
CC       polymerase II during the transition from 'Ser-5' to 'Ser-2'
CC       phosphorylation. {ECO:0000269|PubMed:18408053,
CC       ECO:0000269|PubMed:19394294}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + O-phospho-L-seryl-[protein] = L-seryl-[protein] +
CC         phosphate; Xref=Rhea:RHEA:20629, Rhea:RHEA-COMP:9863, Rhea:RHEA-
CC         COMP:11604, ChEBI:CHEBI:15377, ChEBI:CHEBI:29999, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:83421; EC=3.1.3.16;
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + O-phospho-L-threonyl-[protein] = L-threonyl-[protein] +
CC         phosphate; Xref=Rhea:RHEA:47004, Rhea:RHEA-COMP:11060, Rhea:RHEA-
CC         COMP:11605, ChEBI:CHEBI:15377, ChEBI:CHEBI:30013, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:61977; EC=3.1.3.16;
CC   -!- SUBUNIT: Interacts with RPO21. {ECO:0000269|PubMed:18408053}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Shuttles constitutively
CC       between the cytoplasm and the nucleus.
CC   -!- MISCELLANEOUS: Present with 5480 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the RPAP2 family. {ECO:0000255|PROSITE-
CC       ProRule:PRU00812, ECO:0000305}.
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DR   EMBL; U18917; AAB64666.1; -; Genomic_DNA.
DR   EMBL; BK006939; DAA07800.1; -; Genomic_DNA.
DR   PIR; S50642; S50642.
DR   RefSeq; NP_011066.3; NM_001179029.3.
DR   PDB; 5C2Y; X-ray; 2.60 A; A/B=1-178.
DR   PDBsum; 5C2Y; -.
DR   AlphaFoldDB; P40084; -.
DR   SMR; P40084; -.
DR   BioGRID; 36888; 248.
DR   DIP; DIP-6690N; -.
DR   IntAct; P40084; 9.
DR   MINT; P40084; -.
DR   STRING; 4932.YER139C; -.
DR   iPTMnet; P40084; -.
DR   MaxQB; P40084; -.
DR   PaxDb; 4932-YER139C; -.
DR   PeptideAtlas; P40084; -.
DR   EnsemblFungi; YER139C_mRNA; YER139C; YER139C.
DR   GeneID; 856882; -.
DR   KEGG; sce:YER139C; -.
DR   AGR; SGD:S000000941; -.
DR   SGD; S000000941; RTR1.
DR   VEuPathDB; FungiDB:YER139C; -.
DR   eggNOG; KOG4780; Eukaryota.
DR   HOGENOM; CLU_086709_0_0_1; -.
DR   InParanoid; P40084; -.
DR   OMA; CCKEHYQ; -.
DR   OrthoDB; 1410801at2759; -.
DR   BioCyc; YEAST:G3O-30300-MONOMER; -.
DR   Reactome; R-SCE-6807505; RNA polymerase II transcribes snRNA genes.
DR   BioGRID-ORCS; 856882; 1 hit in 10 CRISPR screens.
DR   PRO; PR:P40084; -.
DR   Proteomes; UP000002311; Chromosome V.
DR   RNAct; P40084; Protein.
DR   GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; IDA:SGD.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0017018; F:myosin phosphatase activity; IEA:UniProtKB-EC.
DR   GO; GO:0043175; F:RNA polymerase core enzyme binding; IEA:InterPro.
DR   GO; GO:0008420; F:RNA polymerase II CTD heptapeptide repeat phosphatase activity; IDA:SGD.
DR   GO; GO:0006366; P:transcription by RNA polymerase II; IMP:SGD.
DR   Gene3D; 1.25.40.820; -; 1.
DR   InterPro; IPR039693; Rtr1/RPAP2.
DR   InterPro; IPR007308; Rtr1/RPAP2_dom.
DR   InterPro; IPR038534; Rtr1/RPAP2_sf.
DR   PANTHER; PTHR14732:SF0; RNA POLYMERASE II SUBUNIT B1 CTD PHOSPHATASE RPAP2-RELATED; 1.
DR   PANTHER; PTHR14732; UNCHARACTERIZED; 1.
DR   Pfam; PF04181; RPAP2_Rtr1; 1.
DR   PROSITE; PS51479; ZF_RTR1; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Hydrolase; Metal-binding; Nucleus;
KW   Protein phosphatase; Reference proteome; Transcription;
KW   Transcription regulation; Zinc; Zinc-finger.
FT   CHAIN           1..226
FT                   /note="RNA polymerase II subunit B1 CTD phosphatase RTR1"
FT                   /id="PRO_0000202653"
FT   ZN_FING         50..136
FT                   /note="RTR1-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00812"
FT   BINDING         73
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00812"
FT   BINDING         78
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00812"
FT   BINDING         112
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00812"
FT   BINDING         116
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00812"
FT   MUTAGEN         73
FT                   /note="C->S: Loss of function."
FT                   /evidence="ECO:0000269|PubMed:18408053"
FT   MUTAGEN         112
FT                   /note="C->S: Loss of function; when associated with S-116."
FT                   /evidence="ECO:0000269|PubMed:18408053"
FT   MUTAGEN         116
FT                   /note="H->S: Loss of function; when associated with S-112."
FT                   /evidence="ECO:0000269|PubMed:18408053"
FT   HELIX           4..11
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           13..15
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           23..37
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   STRAND          38..40
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   STRAND          42..44
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           45..51
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           52..54
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           57..69
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           91..99
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   STRAND          100..102
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           105..108
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   STRAND          111..113
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           114..124
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           132..134
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   TURN            136..139
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           146..152
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           158..165
FT                   /evidence="ECO:0007829|PDB:5C2Y"
FT   HELIX           168..175
FT                   /evidence="ECO:0007829|PDB:5C2Y"
SQ   SEQUENCE   226 AA;  26240 MW;  E234D9ADC18C3FCA CRC64;
     MATIEDIKET ALIPFQKHRQ LSMHEAEVIT LEIIGLLCDS ECKDEKTLKY LGRFLTPDMY
     QDLVDERNLN KRCGYPLCGK SPERIRDPFS MNDTTKKFLL ENNPYAYLSH YCSKFHFRCS
     QFYQVQLSDE ALFARTGVHL FEDPEQDKHD IDFKVTLFEE LLREKASEED IKSLISGLKK
     LGLNPDSGTT EKDDTELEDD LSKWLAQIKI VENDNPSILG DFTRED
//