TYW1_METJA
ID TYW1_METJA Reviewed; 311 AA.
AC Q57705;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase {ECO:0000255|HAMAP-Rule:MF_01921};
DE EC=4.1.3.44 {ECO:0000255|HAMAP-Rule:MF_01921};
DE AltName: Full=MjTYW1;
DE AltName: Full=tRNA wyosine derivatives biosynthesis protein Taw1 {ECO:0000255|HAMAP-Rule:MF_01921};
GN Name=taw1 {ECO:0000255|HAMAP-Rule:MF_01921}; OrderedLocusNames=MJ0257;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP GENE NAME.
RX PubMed=20382657; DOI=10.1093/molbev/msq096;
RA de Crecy-Lagard V., Brochier-Armanet C., Urbonavicius J., Fernandez B.,
RA Phillips G., Lyons B., Noma A., Alvarez S., Droogmans L., Armengaud J.,
RA Grosjean H.;
RT "Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse
RT pathway in Archaea.";
RL Mol. Biol. Evol. 27:2062-2077(2010).
RN [3]
RP CATALYTIC ACTIVITY, AND FUNCTION.
RX PubMed=22026549; DOI=10.1021/bi2015053;
RA Young A.P., Bandarian V.;
RT "Pyruvate is the source of the two carbons that are required for formation
RT of the imidazoline ring of 4-demethylwyosine.";
RL Biochemistry 50:10573-10575(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), COFACTOR, AND SUBUNIT.
RX PubMed=17727881; DOI=10.1016/j.jmb.2007.07.024;
RA Suzuki Y., Noma A., Suzuki T., Senda M., Senda T., Ishitani R., Nureki O.;
RT "Crystal structure of the radical SAM enzyme catalyzing tricyclic modified
RT base formation in tRNA.";
RL J. Mol. Biol. 372:1204-1214(2007).
CC -!- FUNCTION: Component of the wyosine derivatives biosynthesis pathway
CC that catalyzes the condensation of N-methylguanine with 2 carbon atoms
CC from pyruvate to form the tricyclic 4-demethylwyosine (imG-14) on
CC guanosine-37 of tRNA(Phe). {ECO:0000255|HAMAP-Rule:MF_01921,
CC ECO:0000269|PubMed:22026549}.
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; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01921, ECO:0000269|PubMed:22026549};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000305|PubMed:17727881};
CC Note=Binds 2 [4Fe-4S] clusters. Binds 1 [4Fe-4S] cluster coordinated
CC with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000305|PubMed:17727881};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_01921,
CC ECO:0000269|PubMed:17727881}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01921}.
CC -!- SIMILARITY: Belongs to the TYW1 family. {ECO:0000255|HAMAP-
CC Rule:MF_01921}.
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DR EMBL; L77117; AAB98244.1; -; Genomic_DNA.
DR PIR; B64332; B64332.
DR RefSeq; WP_010869754.1; NC_000909.1.
DR PDB; 2Z2U; X-ray; 2.40 A; A=1-311.
DR PDB; 6DJT; X-ray; 1.64 A; A=1-311.
DR PDBsum; 2Z2U; -.
DR PDBsum; 6DJT; -.
DR AlphaFoldDB; Q57705; -.
DR SMR; Q57705; -.
DR STRING; 243232.MJ_0257; -.
DR EnsemblBacteria; AAB98244; AAB98244; MJ_0257.
DR GeneID; 1451111; -.
DR KEGG; mja:MJ_0257; -.
DR eggNOG; arCOG04174; Archaea.
DR HOGENOM; CLU_007952_3_0_2; -.
DR InParanoid; Q57705; -.
DR OMA; HRCLQMT; -.
DR OrthoDB; 36053at2157; -.
DR PhylomeDB; Q57705; -.
DR BRENDA; 4.1.3.44; 3260.
DR EvolutionaryTrace; Q57705; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
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:0008033; P:tRNA processing; IEA:UniProtKB-UniRule.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_01921; TYW1_archaea; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR007197; rSAM.
DR InterPro; IPR013917; tRNA_wybutosine-synth.
DR InterPro; IPR034556; tRNA_wybutosine-synthase.
DR InterPro; IPR023993; TYW1_archaea.
DR PANTHER; PTHR13930; PTHR13930; 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 TIGRFAMs; TIGR03972; rSAM_TYW1; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Cytoplasm; Iron; Iron-sulfur; Lyase; Metal-binding;
KW Reference proteome; S-adenosyl-L-methionine; tRNA processing.
FT CHAIN 1..311
FT /note="S-adenosyl-L-methionine-dependent tRNA 4-
FT demethylwyosine synthase"
FT /id="PRO_0000217862"
FT DOMAIN 45..283
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 26
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 39
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 52
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 62
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000305"
FT BINDING 66
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000305"
FT BINDING 69
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000305"
FT HELIX 4..12
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 16..18
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 21..23
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 27..35
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 40..45
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 52..58
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 92..108
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 109..113
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 114..117
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 119..125
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 130..133
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 145..154
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 158..163
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 168..173
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 177..182
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 188..195
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 199..211
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 212..214
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 215..224
FT /evidence="ECO:0007829|PDB:6DJT"
FT TURN 226..228
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 232..235
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 236..242
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 245..251
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 264..266
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 270..282
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 284..292
FT /evidence="ECO:0007829|PDB:6DJT"
FT HELIX 293..295
FT /evidence="ECO:0007829|PDB:6DJT"
FT STRAND 297..302
FT /evidence="ECO:0007829|PDB:6DJT"
SQ SEQUENCE 311 AA; 36712 MW; 7B05311C25A29F3D CRC64;
MIPEEIYKIL RKQRYQIDGH TAVKLCGWVR KKMLEDKNCY KSKFYGIETH RCIQCTPSVI
WCQQNCIFCW RVLPRDIGID ISQIKEPKWE EPEVVYEKIL AMHKRIIMGY AGVLDRVGEK
KFKEALEPKH VAISLSGEPT LYPYLDELIK IFHKNGFTTF VVSNGILTDV IEKIEPTQLY
ISLDAYDLDS YRRICGGKKE YWESILNTLD ILKEKKRTCI RTTLIRGYND DILKFVELYE
RADVHFIELK SYMHVGYSQK RLKKEDMLQH DEILKLAKML DENSSYKLID DSEDSRVALL
QNENRKINPK L
