TYW1_PYRHO
ID TYW1_PYRHO Reviewed; 342 AA.
AC O59412;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 122.
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=tRNA wyosine derivatives biosynthesis protein Taw1 {ECO:0000255|HAMAP-Rule:MF_01921};
GN Name=taw1 {ECO:0000255|HAMAP-Rule:MF_01921}; OrderedLocusNames=PH1705;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
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 X-RAY CRYSTALLOGRAPHY (2.21 ANGSTROMS), COFACTOR, AND SUBUNIT.
RX PubMed=17881823; DOI=10.1107/s0907444907040668;
RA Goto-Ito S., Ishii R., Ito T., Shibata R., Fusatomi E., Sekine S.I.,
RA Bessho Y., Yokoyama S.;
RT "Structure of an archaeal TYW1, the enzyme catalyzing the second step of
RT wye-base biosynthesis.";
RL Acta Crystallogr. D 63:1059-1068(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 -!- 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};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000305|PubMed:17881823};
CC Note=Binds 1 [2Fe-2S] cluster. {ECO:0000305|PubMed:17881823};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000305|PubMed:17881823};
CC Note=Binds 1 [4Fe-4S] cluster. The [4Fe-4S] cluster is coordinated with
CC 3 cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000305|PubMed:17881823};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_01921,
CC ECO:0000269|PubMed:17881823}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01921}.
CC -!- SIMILARITY: Belongs to the TYW1 family. {ECO:0000255|HAMAP-
CC Rule:MF_01921}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BA000001; BAA30819.1; -; Genomic_DNA.
DR PIR; D71178; D71178.
DR PDB; 2YX0; X-ray; 2.21 A; A=1-342.
DR PDBsum; 2YX0; -.
DR AlphaFoldDB; O59412; -.
DR SMR; O59412; -.
DR IntAct; O59412; 1.
DR MINT; O59412; -.
DR STRING; 70601.3258136; -.
DR EnsemblBacteria; BAA30819; BAA30819; BAA30819.
DR KEGG; pho:PH1705; -.
DR eggNOG; arCOG04174; Archaea.
DR OMA; HRCLQMT; -.
DR BioCyc; MetaCyc:MON-18047; -.
DR BRENDA; 4.1.3.44; 5244.
DR EvolutionaryTrace; O59412; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
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 2Fe-2S; 3D-structure; 4Fe-4S; Cytoplasm; Iron; Iron-sulfur; Lyase;
KW Metal-binding; S-adenosyl-L-methionine; tRNA processing.
FT CHAIN 1..342
FT /note="S-adenosyl-L-methionine-dependent tRNA 4-
FT demethylwyosine synthase"
FT /id="PRO_0000407857"
FT DOMAIN 64..312
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 45
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000305"
FT BINDING 58
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000305"
FT BINDING 71
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000305"
FT BINDING 81
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000305"
FT BINDING 85
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000305"
FT BINDING 88
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000305"
FT HELIX 22..30
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 34..37
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 40..42
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 48..54
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 59..64
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 68..70
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 71..76
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 107..122
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 133..139
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 144..147
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 149..151
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 159..168
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 172..177
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 182..190
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 196..202
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 207..214
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 216..219
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 221..232
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 236..245
FT /evidence="ECO:0007829|PDB:2YX0"
FT TURN 247..249
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 254..264
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 267..273
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 286..288
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 292..303
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 309..315
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 316..318
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 320..325
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 328..333
FT /evidence="ECO:0007829|PDB:2YX0"
FT HELIX 334..336
FT /evidence="ECO:0007829|PDB:2YX0"
FT STRAND 337..339
FT /evidence="ECO:0007829|PDB:2YX0"
SQ SEQUENCE 342 AA; 39840 MW; F321AF462AA262D7 CRC64;
MMEMITIKPG KITVQANPNM PKEVAELFRK QHYEIVGRHS GVKLCHWLKK SLTEGRFCYK
QKFYGIHSHR CLQMTPVLAW CTHNCIFCWR PMENFLGTEL PQPWDDPAFI VEESIKAQRK
LLIGYKGNPK VDKKKFEEAW NPTHAAISLS GEPMLYPYMG DLVEEFHKRG FTTFIVTNGT
IPERLEEMIK EDKLPTQLYV SITAPDIETY NSVNIPMIPD GWERILRFLE LMRDLPTRTV
VRLTLVKGEN MHSPEKYAKL ILKARPMFVE AKAYMFVGYS RNRLTINNMP SHQDIREFAE
ALVKHLPGYH IEDEYEPSRV VLIMRDDVDP QGTGVEGRFI KH
