RTR1_YEAST
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 03-AUG-2022, entry version 155.
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; 244.
DR DIP; DIP-6690N; -.
DR IntAct; P40084; 9.
DR MINT; P40084; -.
DR STRING; 4932.YER139C; -.
DR iPTMnet; P40084; -.
DR MaxQB; P40084; -.
DR PaxDb; P40084; -.
DR PRIDE; P40084; -.
DR EnsemblFungi; YER139C_mRNA; YER139C; YER139C.
DR GeneID; 856882; -.
DR KEGG; sce:YER139C; -.
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 BioCyc; YEAST:G3O-30300-MON; -.
DR Reactome; R-SCE-6807505; RNA polymerase II transcribes snRNA genes.
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:0070940; P:dephosphorylation of RNA polymerase II C-terminal domain; 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; PTHR14732; 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
