PUS1_YEAST
ID PUS1_YEAST Reviewed; 544 AA.
AC Q12211; D6W3F8;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 168.
DE RecName: Full=tRNA pseudouridine synthase 1;
DE EC=5.4.99.- {ECO:0000269|PubMed:14562106, ECO:0000269|PubMed:25219674, ECO:0000269|PubMed:9671058};
DE AltName: Full=tRNA pseudouridylate synthase 1;
DE AltName: Full=tRNA-uridine isomerase 1;
GN Name=PUS1; OrderedLocusNames=YPL212C;
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 [GENOMIC DNA].
RX PubMed=8641292; DOI=10.1002/j.1460-2075.1996.tb00580.x;
RA Simos G., Tekotte H., Grosjean H., Segref A., Sharma K., Tollervey D.,
RA Hurt E.C.;
RT "Nuclear pore proteins are involved in the biogenesis of functional tRNA.";
RL EMBO J. 15:2270-2284(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [3]
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 [4]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=9671058; DOI=10.1017/s1355838298980396;
RA Motorin Y., Keith G., Simon C., Foiret D., Simos G., Hurt E., Grosjean H.;
RT "The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate
RT specificity.";
RL RNA 4:856-869(1998).
RN [5]
RP SUBCELLULAR LOCATION.
RX PubMed=11502169; DOI=10.1021/bi010277r;
RA Grandier-Vazeille X., Bathany K., Chaignepain S., Camougrand N., Manon S.,
RA Schmitter J.-M.;
RT "Yeast mitochondrial dehydrogenases are associated in a supramolecular
RT complex.";
RL Biochemistry 40:9758-9769(2001).
RN [6]
RP ZINC-BINDING.
RX PubMed=9585540; DOI=10.1021/bi972671o;
RA Arluison V., Hountondji C., Robert B., Grosjean H.;
RT "Transfer RNA-pseudouridine synthetase Pus1 of Saccharomyces cerevisiae
RT contains one atom of zinc essential for its native conformation and tRNA
RT recognition.";
RL Biochemistry 37:7268-7276(1998).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=10356324; DOI=10.1006/jmbi.1999.2789;
RA Arluison V., Buckle M., Grosjean H.;
RT "Pseudouridine synthetase Pus1 of Saccharomyces cerevisiae: kinetic
RT characterisation, tRNA structural requirement and real-time analysis of its
RT complex with tRNA.";
RL J. Mol. Biol. 289:491-502(1999).
RN [8]
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 [9]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=25219674; DOI=10.1016/j.cell.2014.08.028;
RA Schwartz S., Bernstein D.A., Mumbach M.R., Jovanovic M., Herbst R.H.,
RA Leon-Ricardo B.X., Engreitz J.M., Guttman M., Satija R., Lander E.S.,
RA Fink G., Regev A.;
RT "Transcriptome-wide mapping reveals widespread dynamic-regulated
RT pseudouridylation of ncRNA and mRNA.";
RL Cell 159:148-162(2014).
RN [10]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=31477916; DOI=10.1038/s41589-019-0353-z;
RA Carlile T.M., Martinez N.M., Schaening C., Su A., Bell T.A., Zinshteyn B.,
RA Gilbert W.V.;
RT "mRNA structure determines modification by pseudouridine synthase 1.";
RL Nat. Chem. Biol. 15:966-974(2019).
CC -!- FUNCTION: Formation of pseudouridine at positions 27 and 28 in the
CC anticodon stem and loop of transfer RNAs; at positions 34 and 36 of
CC intron-containing precursor tRNA(Ile) and at position 35 in the intron-
CC containing tRNA(Tyr) (PubMed:9671058, PubMed:10356324,
CC PubMed:25219674). Catalyzes pseudouridylation at position 44 in U2
CC snRNA (PubMed:25219674). Also catalyzes pseudouridylation of mRNAs
CC (PubMed:25219674, PubMed:31477916). {ECO:0000269|PubMed:10356324,
CC ECO:0000269|PubMed:25219674, ECO:0000269|PubMed:31477916,
CC ECO:0000269|PubMed:9671058}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a uridine in tRNA = a pseudouridine in tRNA;
CC Xref=Rhea:RHEA:54572, Rhea:RHEA-COMP:13339, Rhea:RHEA-COMP:13934,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:65315;
CC Evidence={ECO:0000269|PubMed:10356324, ECO:0000269|PubMed:25219674,
CC ECO:0000269|PubMed:9671058};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=uridine in snRNA = pseudouridine in snRNA;
CC Xref=Rhea:RHEA:51124, Rhea:RHEA-COMP:12891, Rhea:RHEA-COMP:12892,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:65315;
CC Evidence={ECO:0000269|PubMed:25219674};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a uridine in mRNA = a pseudouridine in mRNA;
CC Xref=Rhea:RHEA:56644, Rhea:RHEA-COMP:14658, Rhea:RHEA-COMP:14659,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:65315;
CC Evidence={ECO:0000269|PubMed:25219674, ECO:0000269|PubMed:31477916};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:9585540};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:9585540};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=420 nM for tRNA(Val) {ECO:0000269|PubMed:10356324};
CC KM=740 nM for tRNA(Ile) {ECO:0000269|PubMed:10356324};
CC Note=kcat is 0.4 min(-1) for tRNA(Val) (PubMed:10356324). kcat is 0.5
CC min(-1) for tRNA(Ile) (PubMed:10356324).
CC {ECO:0000269|PubMed:10356324};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11502169}.
CC -!- MISCELLANEOUS: Present with 8130 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the tRNA pseudouridine synthase TruA family.
CC {ECO:0000305}.
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DR EMBL; X80673; CAA56698.1; -; Genomic_DNA.
DR EMBL; Z73568; CAA97927.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11224.1; -; Genomic_DNA.
DR PIR; S65231; S65231.
DR RefSeq; NP_015112.1; NM_001184026.1.
DR PDB; 7R9F; X-ray; 2.89 A; A=1-544.
DR PDB; 7R9G; X-ray; 2.40 A; A=1-544.
DR PDBsum; 7R9F; -.
DR PDBsum; 7R9G; -.
DR AlphaFoldDB; Q12211; -.
DR SMR; Q12211; -.
DR BioGRID; 35973; 110.
DR DIP; DIP-5344N; -.
DR IntAct; Q12211; 24.
DR MINT; Q12211; -.
DR STRING; 4932.YPL212C; -.
DR iPTMnet; Q12211; -.
DR MaxQB; Q12211; -.
DR PaxDb; Q12211; -.
DR PRIDE; Q12211; -.
DR EnsemblFungi; YPL212C_mRNA; YPL212C; YPL212C.
DR GeneID; 855889; -.
DR KEGG; sce:YPL212C; -.
DR SGD; S000006133; PUS1.
DR VEuPathDB; FungiDB:YPL212C; -.
DR eggNOG; KOG2553; Eukaryota.
DR GeneTree; ENSGT00950000183160; -.
DR HOGENOM; CLU_021971_0_1_1; -.
DR InParanoid; Q12211; -.
DR OMA; AVMIGYC; -.
DR BioCyc; MetaCyc:YPL212C-MON; -.
DR BioCyc; YEAST:YPL212C-MON; -.
DR BRENDA; 5.4.99.B22; 984.
DR PRO; PR:Q12211; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q12211; protein.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0003729; F:mRNA binding; HDA:SGD.
DR GO; GO:0009982; F:pseudouridine synthase activity; IDA:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:1990481; P:mRNA pseudouridine synthesis; IMP:SGD.
DR GO; GO:0031120; P:snRNA pseudouridine synthesis; IMP:SGD.
DR GO; GO:0006400; P:tRNA modification; TAS:Reactome.
DR GO; GO:0031119; P:tRNA pseudouridine synthesis; IDA:SGD.
DR CDD; cd02568; PseudoU_synth_PUS1_PUS2; 1.
DR Gene3D; 3.30.70.580; -; 1.
DR Gene3D; 3.30.70.660; -; 1.
DR InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR InterPro; IPR001406; PsdUridine_synth_TruA.
DR InterPro; IPR020097; PsdUridine_synth_TruA_a/b_dom.
DR InterPro; IPR020095; PsdUridine_synth_TruA_C.
DR InterPro; IPR041708; PUS1/PUS2-like.
DR InterPro; IPR020094; TruA/RsuA/RluB/E/F_N.
DR PANTHER; PTHR11142; PTHR11142; 1.
DR Pfam; PF01416; PseudoU_synth_1; 1.
DR SUPFAM; SSF55120; SSF55120; 1.
DR TIGRFAMs; TIGR00071; hisT_truA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isomerase; mRNA processing; Nucleus; Reference proteome;
KW tRNA processing; Zinc.
FT CHAIN 1..544
FT /note="tRNA pseudouridine synthase 1"
FT /id="PRO_0000057530"
FT REGION 1..74
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 495..544
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 504..523
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 524..538
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 134
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P07649"
FT STRAND 75..83
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 100..111
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 128..130
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 138..148
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 155..161
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 167..174
FT /evidence="ECO:0007829|PDB:7R9G"
FT TURN 181..184
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 187..195
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 196..199
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 207..213
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 227..241
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 268..285
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 291..302
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 306..309
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 311..313
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 314..316
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 322..324
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 325..333
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 337..339
FT /evidence="ECO:0007829|PDB:7R9G"
FT TURN 340..343
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 344..354
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 360..374
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 380..383
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 386..388
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 397..399
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 400..406
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 408..414
FT /evidence="ECO:0007829|PDB:7R9G"
FT TURN 415..418
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 424..426
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 428..438
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 440..450
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 452..461
FT /evidence="ECO:0007829|PDB:7R9G"
FT HELIX 485..488
FT /evidence="ECO:0007829|PDB:7R9G"
FT STRAND 490..492
FT /evidence="ECO:0007829|PDB:7R9G"
SQ SEQUENCE 544 AA; 62143 MW; 1A7E449601C26EFD CRC64;
MSEENLRPAY DDQVNEDVYK RGAQSKLTKA RKADFDDEKD KKKDNDKHID KRPKSGPRLD
ENGNPLPKEP RLPKRKVAVM VGYCGTGYHG MQYNPPNPTI ESALFKAFVE AGAISKDNSN
DLKKNGFMRA ARTDKGVHAG GNLISLKMII EDPDIKQKIN EKLPEGIRVW DIERVNKAFD
CRKMCSSRWY EYLLPTYSLI GPKPGSILYR DIEESKTELP GVLDEDLESK EFWEEFKKDA
NEKFSTEEIE AILAYVPPAR DEFDINEELY QKVKKYKQLE NAHRRRYRIS AAKLAKFRAS
TSQYLGAHNF HNFTLGKDFK EPSAIRFMKD IKVSDPFVIG DAQTEWISIK IHGQSFMLHQ
IRKMVSMATL ITRCGCPVER ISQAYGQQKI NIPKAPALGL LLEAPVFEGY NKRLEQFGYK
AIDFSKYQDE VDKFKMKHIY DKIYKEEVDE NVFNAFFSYI DSFNKVTGAQ GEETADKSGP
AVQKSIFEFL TAKGIPGLTD APESNKKIKQ RKRMEEEEAA SKKAEISSTT QSNEPEVQPE
AAAN
