TPA1_YEAST
ID TPA1_YEAST Reviewed; 644 AA.
AC P40032; D3DLV1;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=Prolyl 3,4-dihydroxylase TPA1 {ECO:0000303|PubMed:16809762};
DE EC=1.14.11.- {ECO:0000269|PubMed:24550462};
DE AltName: Full=Termination and polyadenylation protein 1 {ECO:0000303|PubMed:16809762};
DE AltName: Full=uS12 prolyl 3,4-dihydroxylase {ECO:0000303|PubMed:25728928};
GN Name=TPA1 {ECO:0000303|PubMed:16809762};
GN OrderedLocusNames=YER049W {ECO:0000312|SGD:S000000851};
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, AND INTERACTION WITH PAB1; SUP1 AND SUP35.
RX PubMed=16809762; DOI=10.1128/mcb.02448-05;
RA Keeling K.M., Salas-Marco J., Osherovich L.Z., Bedwell D.M.;
RT "Tpa1p is part of an mRNP complex that influences translation termination,
RT mRNA deadenylation, and mRNA turnover in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 26:5237-5248(2006).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-607, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND INTERACTION WITH FRK1.
RX PubMed=20489023; DOI=10.1126/science.1176495;
RA Breitkreutz A., Choi H., Sharom J.R., Boucher L., Neduva V., Larsen B.,
RA Lin Z.Y., Breitkreutz B.J., Stark C., Liu G., Ahn J., Dewar-Darch D.,
RA Reguly T., Tang X., Almeida R., Qin Z.S., Pawson T., Gingras A.C.,
RA Nesvizhskii A.I., Tyers M.;
RT "A global protein kinase and phosphatase interaction network in yeast.";
RL Science 328:1043-1046(2010).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF 159-ASP--HIS-161.
RX PubMed=24550462; DOI=10.1073/pnas.1311750111;
RA Loenarz C., Sekirnik R., Thalhammer A., Ge W., Spivakovsky E.,
RA Mackeen M.M., McDonough M.A., Cockman M.E., Kessler B.M., Ratcliffe P.J.,
RA Wolf A., Schofield C.J.;
RT "Hydroxylation of the eukaryotic ribosomal decoding center affects
RT translational accuracy.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:4019-4024(2014).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) OF 1-644, FUNCTION, DISRUPTION
RP PHENOTYPE, SUBUNIT, MUTAGENESIS OF 159-ASP--HIS-161, AND INTERACTION WITH
RP ETT1.
RX PubMed=20630870; DOI=10.1074/jbc.m110.106864;
RA Henri J., Rispal D., Bayart E., van Tilbeurgh H., Seraphin B., Graille M.;
RT "Structural and functional insights into Saccharomyces cerevisiae Tpa1, a
RT putative prolylhydroxylase influencing translation termination and
RT transcription.";
RL J. Biol. Chem. 285:30767-30778(2010).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.77 ANGSTROMS) OF 21-644 IN COMPLEX WITH IRON AND
RP 2-OXOGLUTARATE, AND SUBUNIT.
RX PubMed=20040577; DOI=10.1093/nar/gkp1151;
RA Kim H.S., Kim H.L., Kim K.H., Kim D.J., Lee S.J., Yoon J.Y., Yoon H.J.,
RA Lee H.Y., Park S.B., Kim S.J., Lee J.Y., Suh S.W.;
RT "Crystal structure of Tpa1 from Saccharomyces cerevisiae, a component of
RT the messenger ribonucleoprotein complex.";
RL Nucleic Acids Res. 38:2099-2110(2010).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 21-644 IN COMPLEX WITH
RP INHIBITORS, AND SUBUNIT.
RX PubMed=25728928; DOI=10.1016/j.str.2015.01.014;
RA Horita S., Scotti J.S., Thinnes C., Mottaghi-Taromsari Y.S., Thalhammer A.,
RA Ge W., Aik W., Loenarz C., Schofield C.J., McDonough M.A.;
RT "Structure of the ribosomal oxygenase OGFOD1 provides insights into the
RT regio- and stereoselectivity of prolyl hydroxylases.";
RL Structure 23:639-652(2015).
CC -!- FUNCTION: Prolyl 3,4-dihydroxylase that catalyzes 3,4-dihydroxylation
CC of 'Pro-64' of small ribosomal subunit uS12 (RPS23A and RPS23B),
CC thereby regulating protein translation termination efficiency. Part of
CC a messenger ribonucleoprotein (mRNP) complex at the 3'-UTR of mRNAs. It
CC associates specifically with components of the translation termination
CC complex and is involved in both translation termination and in
CC regulation of normal mRNA decay through translation termination-coupled
CC poly(A) shortening. {ECO:0000269|PubMed:16809762,
CC ECO:0000269|PubMed:20630870, ECO:0000269|PubMed:24550462}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + [ribosomal protein uS12]-L-proline + O2 =
CC [ribosomal protein uS12]-(3S)-3-hydroxy-L-proline + CO2 + succinate;
CC Xref=Rhea:RHEA:54156, Rhea:RHEA-COMP:13816, Rhea:RHEA-COMP:13818,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:50342, ChEBI:CHEBI:85428;
CC Evidence={ECO:0000269|PubMed:24550462, ECO:0000305|PubMed:25728928};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + [ribosomal protein uS12]-(3S)-3-hydroxy-L-
CC proline + O2 = [ribosomal protein uS12]-(3S)-3,4-dihydroxy-L-proline
CC + CO2 + succinate; Xref=Rhea:RHEA:54160, Rhea:RHEA-COMP:13817,
CC Rhea:RHEA-COMP:13818, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:30031, ChEBI:CHEBI:85428,
CC ChEBI:CHEBI:138052; Evidence={ECO:0000269|PubMed:24550462,
CC ECO:0000305|PubMed:25728928};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:20040577};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000269|PubMed:20040577};
CC -!- COFACTOR:
CC Name=L-ascorbate; Xref=ChEBI:CHEBI:38290; Evidence={ECO:0000305};
CC -!- SUBUNIT: Monomer and homodimer (PubMed:20630870, PubMed:20040577).
CC Interacts with FRK1, eRF1 (SUP1), eRF3 (SUP35) and polyadenylate-
CC binding protein PAB1. Interacts with ETT1 (PubMed:16809762,
CC PubMed:20489023). {ECO:0000269|PubMed:16809762,
CC ECO:0000269|PubMed:20040577, ECO:0000269|PubMed:20489023,
CC ECO:0000269|PubMed:20630870}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095}.
CC -!- DISRUPTION PHENOTYPE: Decrease of translation termination efficacy and
CC an increase in mRNAs half-lives and longer mRNA poly(A) tails.
CC {ECO:0000269|PubMed:20630870}.
CC -!- MISCELLANEOUS: Present with 8910 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the TPA1 family. {ECO:0000305}.
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DR EMBL; U18796; AAB64584.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07705.1; -; Genomic_DNA.
DR PIR; S50552; S50552.
DR RefSeq; NP_010969.1; NM_001178940.1.
DR PDB; 3KT1; X-ray; 2.50 A; A=21-644.
DR PDB; 3KT4; X-ray; 2.73 A; A=21-644.
DR PDB; 3KT7; X-ray; 1.77 A; A=21-644.
DR PDB; 3MGU; X-ray; 2.80 A; A=1-644.
DR PDB; 4NHK; X-ray; 1.90 A; A=21-644.
DR PDB; 4NHL; X-ray; 2.84 A; A=21-644.
DR PDB; 4NHM; X-ray; 1.90 A; A=21-644.
DR PDBsum; 3KT1; -.
DR PDBsum; 3KT4; -.
DR PDBsum; 3KT7; -.
DR PDBsum; 3MGU; -.
DR PDBsum; 4NHK; -.
DR PDBsum; 4NHL; -.
DR PDBsum; 4NHM; -.
DR AlphaFoldDB; P40032; -.
DR SMR; P40032; -.
DR BioGRID; 36788; 107.
DR DIP; DIP-2878N; -.
DR IntAct; P40032; 6.
DR MINT; P40032; -.
DR STRING; 4932.YER049W; -.
DR iPTMnet; P40032; -.
DR MaxQB; P40032; -.
DR PaxDb; P40032; -.
DR PRIDE; P40032; -.
DR EnsemblFungi; YER049W_mRNA; YER049W; YER049W.
DR GeneID; 856775; -.
DR KEGG; sce:YER049W; -.
DR SGD; S000000851; TPA1.
DR VEuPathDB; FungiDB:YER049W; -.
DR eggNOG; KOG3844; Eukaryota.
DR GeneTree; ENSGT00390000002349; -.
DR HOGENOM; CLU_017005_0_0_1; -.
DR InParanoid; P40032; -.
DR OMA; YMAGDDD; -.
DR BioCyc; YEAST:G3O-30228-MON; -.
DR EvolutionaryTrace; P40032; -.
DR PRO; PR:P40032; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P40032; protein.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0008198; F:ferrous iron binding; IMP:SGD.
DR GO; GO:0031418; F:L-ascorbic acid binding; IEA:UniProtKB-KW.
DR GO; GO:0031543; F:peptidyl-proline dioxygenase activity; IDA:UniProtKB.
DR GO; GO:0008143; F:poly(A) binding; IDA:SGD.
DR GO; GO:0000288; P:nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; IMP:SGD.
DR GO; GO:0018188; P:peptidyl-proline di-hydroxylation; IDA:UniProtKB.
DR GO; GO:0019511; P:peptidyl-proline hydroxylation; IBA:GO_Central.
DR GO; GO:0006450; P:regulation of translational fidelity; IMP:SGD.
DR GO; GO:0006449; P:regulation of translational termination; IMP:UniProtKB.
DR GO; GO:0006415; P:translational termination; IMP:SGD.
DR Gene3D; 3.60.130.20; -; 1.
DR InterPro; IPR005123; Oxoglu/Fe-dep_dioxygenase.
DR InterPro; IPR019601; Oxoglutarate/Fe-dep_Oase_C.
DR InterPro; IPR006620; Pro_4_hyd_alph.
DR InterPro; IPR043044; TPA1/Ofd1_C.
DR InterPro; IPR039558; TPA1/OFD1_N.
DR Pfam; PF13661; 2OG-FeII_Oxy_4; 1.
DR Pfam; PF10637; Ofd1_CTDD; 1.
DR SMART; SM00702; P4Hc; 1.
DR PROSITE; PS51471; FE2OG_OXY; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Dioxygenase; Iron; Metal-binding; Nucleus; Oxidoreductase;
KW Phosphoprotein; Reference proteome; Vitamin C.
FT CHAIN 1..644
FT /note="Prolyl 3,4-dihydroxylase TPA1"
FT /id="PRO_0000206670"
FT DOMAIN 141..247
FT /note="Fe2OG dioxygenase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805"
FT BINDING 159
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805,
FT ECO:0000269|PubMed:20040577, ECO:0000269|PubMed:25728928"
FT BINDING 161
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805,
FT ECO:0000269|PubMed:20040577, ECO:0000269|PubMed:25728928"
FT BINDING 173
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000269|PubMed:20040577"
FT BINDING 227
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805,
FT ECO:0000269|PubMed:20040577, ECO:0000269|PubMed:25728928"
FT BINDING 238
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00805,
FT ECO:0000269|PubMed:20040577"
FT MOD_RES 607
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MUTAGEN 159..161
FT /note="HDD->ADN,ADA: Loss of function."
FT /evidence="ECO:0000269|PubMed:20630870,
FT ECO:0000269|PubMed:24550462"
FT MUTAGEN 159
FT /note="H->A: Loss of function."
FT HELIX 27..29
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 32..35
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 37..48
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 56..60
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 64..77
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 81..84
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 86..92
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 111..120
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 123..132
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 139..142
FT /evidence="ECO:0007829|PDB:3MGU"
FT STRAND 145..150
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 155..159
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 166..173
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 183..185
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 194..196
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 205..208
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 214..219
FT /evidence="ECO:0007829|PDB:3KT7"
FT TURN 222..224
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 238..246
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 252..254
FT /evidence="ECO:0007829|PDB:4NHK"
FT HELIX 259..268
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 269..277
FT /evidence="ECO:0007829|PDB:3KT4"
FT HELIX 278..282
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 294..304
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 332..339
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 344..346
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 349..362
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 363..369
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 373..389
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 396..398
FT /evidence="ECO:0007829|PDB:3KT7"
FT TURN 409..411
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 415..417
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 419..421
FT /evidence="ECO:0007829|PDB:3KT1"
FT HELIX 428..436
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 443..457
FT /evidence="ECO:0007829|PDB:3KT7"
FT TURN 461..463
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 466..479
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 481..491
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 492..495
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 497..505
FT /evidence="ECO:0007829|PDB:3KT7"
FT TURN 507..509
FT /evidence="ECO:0007829|PDB:3KT7"
FT HELIX 521..523
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 527..540
FT /evidence="ECO:0007829|PDB:3KT7"
FT TURN 546..550
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 555..558
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 588..592
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 596..604
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 609..612
FT /evidence="ECO:0007829|PDB:3KT7"
FT STRAND 623..634
FT /evidence="ECO:0007829|PDB:3KT7"
SQ SEQUENCE 644 AA; 74041 MW; 1273410E75479A46 CRC64;
MKRKTAEVKG EKERNSKQIS LEEDKIKGMF NPKIWDKTFQ DGLKKEIEDS QPYNWGTIHE
LVNDDLLRAV RKEIETEIHF TKKETDIYRV NQSGDLANLS GLDWDDLSRL PNLFKLRQIL
YSKQYRDFFG YVTKAGKLSG SKTDMSINTY TKGCHLLTHD DVIGSRRISF ILYLPDPDRK
WKSHYGGGLR LFPSILPNVP HSDPSAKLVP QFNQIAFFKV LPGFSFHDVE EVKVDKHRLS
IQGWYHIPQV GEEGYIPGEE EAWVRNNTST LAQIESNVLE DFEFPKDERN ILSFHEVKHF
EKMLKGDAGA KTDNTPKESM TSVISDSVKL SEAEFTYLSQ YISPEHLSSK GIEKLQKQFV
ENSSLQIESF LNDDKSELLK KVIKQKELEQ ECPYHSKDVK APWKTAIPPH KARYLYIDGK
EYRNFQTEAD ILEALNNNDL PNFQFTKDAI KIISDASGNS RENNFDAELA LIDLAVFHKS
TIFKKYLALL TSLCPVSEQI LIRRFRPGMD FTLATKCRFN ELLKSNPDII DAVLEGTLCL
TPSAGWESGE LGGYELYMMD DDEDNKQYLK EDVEDASVYR ADDSGDSVLI NDPPAWNTFN
LVLRDESVLE FVKYVSWSAK SSRWDVKMKW DVKSCDEDGQ EDEA
