TYW1_YEAST
ID TYW1_YEAST Reviewed; 810 AA.
AC Q08960; D6W3G3;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 173.
DE RecName: Full=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase;
DE EC=4.1.3.44;
DE AltName: Full=tRNA wybutosine-synthesizing protein 1;
GN Name=TYW1; OrderedLocusNames=YPL207W;
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=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 [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 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 [4]
RP UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-496, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RC STRAIN=SUB592;
RX PubMed=12872131; DOI=10.1038/nbt849;
RA Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G.,
RA Roelofs J., Finley D., Gygi S.P.;
RT "A proteomics approach to understanding protein ubiquitination.";
RL Nat. Biotechnol. 21:921-926(2003).
RN [5]
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 [6]
RP FUNCTION.
RX PubMed=16162496; DOI=10.1074/jbc.m506939200;
RA Waas W.F., de Crecy-Lagard V., Schimmel P.;
RT "Discovery of a gene family critical to wyosine base formation in a subset
RT of phenylalanine-specific transfer RNAs.";
RL J. Biol. Chem. 280:37616-37622(2005).
RN [7]
RP FUNCTION, COFACTOR, AND MUTAGENESIS OF CYS-479; CYS-483; CYS-486; GLU-532
RP AND GLU-550.
RX PubMed=16642040; DOI=10.1038/sj.emboj.7601105;
RA Noma A., Kirino Y., Ikeuchi Y., Suzuki T.;
RT "Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic
RT phenylalanine tRNA.";
RL EMBO J. 25:2142-2154(2006).
CC -!- FUNCTION: Component of the wybutosine biosynthesis pathway. Wybutosine
CC is a hyper modified guanosine with a tricyclic base found at the 3'-
CC position adjacent to the anticodon of eukaryotic phenylalanine tRNA.
CC Catalyzes the condensation of N-methylguanine with 2 carbon atoms from
CC pyruvate to form the tricyclic 4-demethylwyosine, an intermediate in
CC wybutosine biosynthesis (By similarity). {ECO:0000250,
CC ECO:0000269|PubMed:16162496, ECO:0000269|PubMed:16642040}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=N(1)-methylguanosine(37) in tRNA(Phe) + pyruvate + S-adenosyl-
CC L-methionine = 4-demethylwyosine(37) in tRNA(Phe) + 5'-deoxyadenosine
CC + CO2 + H2O + L-methionine; Xref=Rhea:RHEA:36347, Rhea:RHEA-
CC COMP:10164, Rhea:RHEA-COMP:10165, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:16526, ChEBI:CHEBI:17319,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:59789, ChEBI:CHEBI:64315,
CC ChEBI:CHEBI:73542; EC=4.1.3.44;
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:16642040};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000269|PubMed:16642040};
CC -!- PATHWAY: tRNA modification; wybutosine-tRNA(Phe) biosynthesis.
CC -!- SUBCELLULAR LOCATION: Endoplasmic reticulum
CC {ECO:0000269|PubMed:14562095}.
CC -!- MISCELLANEOUS: Present with 5410 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the TYW1 family. {ECO:0000305}.
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DR EMBL; Z73563; CAA97922.1; -; Genomic_DNA.
DR EMBL; Z73562; CAA97921.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11229.1; -; Genomic_DNA.
DR PIR; S65226; S65226.
DR RefSeq; NP_015117.1; NM_001184021.1.
DR AlphaFoldDB; Q08960; -.
DR SMR; Q08960; -.
DR BioGRID; 35978; 63.
DR DIP; DIP-3972N; -.
DR IntAct; Q08960; 8.
DR MINT; Q08960; -.
DR STRING; 4932.YPL207W; -.
DR iPTMnet; Q08960; -.
DR MaxQB; Q08960; -.
DR PaxDb; Q08960; -.
DR PRIDE; Q08960; -.
DR EnsemblFungi; YPL207W_mRNA; YPL207W; YPL207W.
DR GeneID; 855894; -.
DR KEGG; sce:YPL207W; -.
DR SGD; S000006128; TYW1.
DR VEuPathDB; FungiDB:YPL207W; -.
DR eggNOG; KOG1160; Eukaryota.
DR GeneTree; ENSGT00510000047059; -.
DR HOGENOM; CLU_007952_1_2_1; -.
DR InParanoid; Q08960; -.
DR OMA; LPCFVEI; -.
DR BioCyc; MetaCyc:G3O-34098-MON; -.
DR BioCyc; YEAST:G3O-34098-MON; -.
DR BRENDA; 4.1.3.44; 984.
DR UniPathway; UPA00375; -.
DR PRO; PR:Q08960; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; Q08960; protein.
DR GO; GO:0005737; C:cytoplasm; TAS:Reactome.
DR GO; GO:0005783; C:endoplasmic reticulum; HDA:SGD.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0010181; F:FMN binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0102521; F:tRNA-4-demethylwyosine synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0031591; P:wybutosine biosynthetic process; IMP:SGD.
DR Gene3D; 3.20.20.70; -; 1.
DR Gene3D; 3.40.50.360; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR008254; Flavodoxin/NO_synth.
DR InterPro; IPR029039; Flavoprotein-like_sf.
DR InterPro; IPR007197; rSAM.
DR InterPro; IPR013917; tRNA_wybutosine-synth.
DR InterPro; IPR034556; tRNA_wybutosine-synthase.
DR PANTHER; PTHR13930; PTHR13930; 1.
DR Pfam; PF00258; Flavodoxin_1; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR Pfam; PF08608; Wyosine_form; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SFLD; SFLDF00284; tRNA_wybutosine-synthesizing; 1.
DR SUPFAM; SSF52218; SSF52218; 1.
DR PROSITE; PS50902; FLAVODOXIN_LIKE; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Endoplasmic reticulum; Iron; Iron-sulfur; Isopeptide bond; Lyase;
KW Metal-binding; Nucleotide-binding; Reference proteome;
KW S-adenosyl-L-methionine; tRNA processing; Ubl conjugation.
FT CHAIN 1..810
FT /note="S-adenosyl-L-methionine-dependent tRNA 4-
FT demethylwyosine synthase"
FT /id="PRO_0000217861"
FT DOMAIN 205..360
FT /note="Flavodoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT DOMAIN 463..713
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT REGION 86..116
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 156..176
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 374..407
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 782..810
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 159..176
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 374..392
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 782..797
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 211..215
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 304..337
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00088"
FT BINDING 479
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 483
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 486
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT CROSSLNK 496
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000269|PubMed:12872131"
FT MUTAGEN 479
FT /note="C->A: Loss of function."
FT /evidence="ECO:0000269|PubMed:16642040"
FT MUTAGEN 483
FT /note="C->A: Loss of function."
FT /evidence="ECO:0000269|PubMed:16642040"
FT MUTAGEN 486
FT /note="C->A: Loss of function."
FT /evidence="ECO:0000269|PubMed:16642040"
FT MUTAGEN 532
FT /note="E->A: No effect."
FT /evidence="ECO:0000269|PubMed:16642040"
FT MUTAGEN 550
FT /note="E->A: Loss of function."
FT /evidence="ECO:0000269|PubMed:16642040"
SQ SEQUENCE 810 AA; 89805 MW; C6A18C949B6E5F8B CRC64;
MDGFRVAGAL VVGALTAAYL YFGGRFSIAL VIIVGYGIYC NEASGGSQDS QEKLDLNKQQ
KKPCCSDKKI ADGGKKTGGC CSDKKNGGGK GGGCCSSKGG KKGGCCSSKG GKKGGCCSSK
KNIGDNENTA TEVEKAVNYP VTVDFTEVFR KPTKKRSSTP KVFSKNSSSN SRVGKKLSVS
KKIGPDGLIK SALTISNETL LSSQIYVLYS SLQGAASKAA KSVYDKLKEL DELTNEPKLL
NLDDLSDFDD YFINVPVENA LYVLVLPSYD IDCPLDYFLQ TLEENANDFR VDSFPLRKLV
GYTVLGLGDS ESWPEKFCYQ AKRADHWISR LGGRRIFPLG KVCMKTGGSA KIDEWTSLLA
ETLKDDEPII YEYDENADSE EDEEEGNGSD ELGDVEDIGG KGSNGKFSGA DEIKQMVAKD
SPTYKNLTKQ GYKVIGSHSG VKICRWTKNE LRGKGSCYKK SLFNIASSRC MELTPSLACS
SKCVFCWRHG TNPVSKNWRW EVDEPEYILE NALKGHYSMI KQMRGVPGVI AERFAKAFEV
RHCALSLVGE PILYPHINKF IQLLHQKGIT SFLVCNAQHP EALRNIVKVT QLYVSIDAPT
KTELKKVDRP LYKDFWERMV ECLEILKTVQ NHQRTVFRLT LVKGFNMGDV SAYADLVQRG
LPGFIEVKGA TFSGSSDGNG NPLTMQNIPF YEECVKFVKA FTTELQRRGL HYDLAAEHAH
SNCLLIADTK FKINGEWHTH IDFDKFFVLL NSGKDFTYMD YLEKTPEWAL FGNGGFAPGN
TRVYRKDKKK QNKENQETTT RETPLPPIPA
