TYW2_PYRHO
ID TYW2_PYRHO Reviewed; 278 AA.
AC O58523;
DT 03-MAY-2011, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase {ECO:0000255|HAMAP-Rule:MF_01922};
DE EC=2.5.1.114 {ECO:0000255|HAMAP-Rule:MF_01922};
DE AltName: Full=PhTYW2;
DE AltName: Full=tRNA wyosine derivatives biosynthesis protein Taw2 {ECO:0000255|HAMAP-Rule:MF_01922};
GN Name=taw2 {ECO:0000255|HAMAP-Rule:MF_01922}; OrderedLocusNames=PH0793;
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 (2.30 ANGSTROMS) IN COMPLEXES WITH
RP S-ADENOSYL-L-METHIONINE AND 5'-DEOXY-5'-METHYLTHIOADENOSINE, FUNCTION,
RP CATALYTIC ACTIVITY, PATHWAY, AND MUTAGENESIS OF ARG-76; MET-107; ASN-112;
RP ARG-116; HIS-138; PRO-142; GLU-155; ASP-183 AND GLY-199.
RX PubMed=19717466; DOI=10.1073/pnas.0905270106;
RA Umitsu M., Nishimasu H., Noma A., Suzuki T., Ishitani R., Nureki O.;
RT "Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction
RT catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:15616-15621(2009).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS).
RG Midwest center for structural genomics (MCSG);
RT "Crystal structure of protein PH0793 from Pyrococcus horikoshii.";
RL Submitted (OCT-2009) to the PDB data bank.
CC -!- FUNCTION: S-adenosyl-L-methionine-dependent transferase that acts as a
CC component of the wyosine derivatives biosynthesis pathway. Catalyzes
CC the transfer of the alpha-amino-alpha-carboxypropyl (acp) group from S-
CC adenosyl-L-methionine to 4-demethylwyosine (imG-14), forming 7-
CC aminocarboxypropyl-demethylwyosine (wybutosine-86) at position 37 of
CC tRNA(Phe). {ECO:0000255|HAMAP-Rule:MF_01922,
CC ECO:0000269|PubMed:19717466}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-demethylwyosine(37) in tRNA(Phe) + S-adenosyl-L-methionine =
CC 4-demethyl-7-[(3S)-3-amino-3-carboxypropyl]wyosine(37) in tRNA(Phe) +
CC H(+) + S-methyl-5'-thioadenosine; Xref=Rhea:RHEA:36355, Rhea:RHEA-
CC COMP:10164, Rhea:RHEA-COMP:10378, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:17509, ChEBI:CHEBI:59789, ChEBI:CHEBI:64315,
CC ChEBI:CHEBI:73550; EC=2.5.1.114; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01922, ECO:0000269|PubMed:19717466};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01922}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. TRM5/TYW2 family. {ECO:0000255|HAMAP-Rule:MF_01922}.
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DR EMBL; BA000001; BAA29886.1; -; Genomic_DNA.
DR PIR; D71128; D71128.
DR RefSeq; WP_010884887.1; NC_000961.1.
DR PDB; 3A25; X-ray; 2.30 A; A=1-278.
DR PDB; 3A26; X-ray; 2.50 A; A=1-278.
DR PDB; 3K6R; X-ray; 2.10 A; A=1-278.
DR PDBsum; 3A25; -.
DR PDBsum; 3A26; -.
DR PDBsum; 3K6R; -.
DR AlphaFoldDB; O58523; -.
DR SMR; O58523; -.
DR STRING; 70601.3257203; -.
DR EnsemblBacteria; BAA29886; BAA29886; BAA29886.
DR GeneID; 1443122; -.
DR KEGG; pho:PH0793; -.
DR eggNOG; arCOG10124; Archaea.
DR OMA; IHYHETV; -.
DR OrthoDB; 55502at2157; -.
DR BioCyc; MetaCyc:MON-18048; -.
DR BRENDA; 2.5.1.114; 5244.
DR EvolutionaryTrace; O58523; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016765; F:transferase activity, transferring alkyl or aryl (other than methyl) groups; IDA:UniProtKB.
DR GO; GO:0102522; F:tRNA 4-demethylwyosine alpha-amino-alpha-carboxypropyltransferase activity; IEA:UniProtKB-EC.
DR GO; GO:0006400; P:tRNA modification; IDA:UniProtKB.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_01922; TYW2_archaea; 1.
DR InterPro; IPR030382; MeTrfase_TRM5/TYW2.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR030867; TYW2_archaea.
DR Pfam; PF02475; Met_10; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51684; SAM_MT_TRM5_TYW2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; S-adenosyl-L-methionine; Transferase;
KW tRNA processing.
FT CHAIN 1..278
FT /note="tRNA(Phe) (4-demethylwyosine(37)-C(7))
FT aminocarboxypropyltransferase"
FT /id="PRO_0000407849"
FT BINDING 109
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 116
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 155
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 183..184
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT MUTAGEN 76
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:19717466"
FT MUTAGEN 107
FT /note="M->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:19717466"
FT MUTAGEN 112
FT /note="N->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:19717466"
FT MUTAGEN 116
FT /note="R->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:19717466"
FT MUTAGEN 138
FT /note="H->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:19717466"
FT MUTAGEN 142
FT /note="P->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:19717466"
FT MUTAGEN 155
FT /note="E->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:19717466"
FT MUTAGEN 183
FT /note="D->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:19717466"
FT MUTAGEN 199
FT /note="G->N: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:19717466"
FT HELIX 7..14
FT /evidence="ECO:0007829|PDB:3K6R"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 20..25
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 31..33
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 36..39
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 46..48
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 49..60
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 63..67
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 81..84
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 89..94
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 97..102
FT /evidence="ECO:0007829|PDB:3K6R"
FT TURN 103..105
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 110..112
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 113..122
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 128..131
FT /evidence="ECO:0007829|PDB:3K6R"
FT TURN 135..139
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 140..145
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 150..154
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 158..170
FT /evidence="ECO:0007829|PDB:3K6R"
FT TURN 174..176
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 177..180
FT /evidence="ECO:0007829|PDB:3K6R"
FT TURN 184..186
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 193..198
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 204..207
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 208..214
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 215..228
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:3K6R"
FT TURN 232..236
FT /evidence="ECO:0007829|PDB:3K6R"
FT HELIX 237..246
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 250..262
FT /evidence="ECO:0007829|PDB:3K6R"
FT TURN 263..265
FT /evidence="ECO:0007829|PDB:3K6R"
FT STRAND 266..276
FT /evidence="ECO:0007829|PDB:3K6R"
SQ SEQUENCE 278 AA; 32151 MW; 392887387506C3F8 CRC64;
MRTQGIKPRI REILSKELPE ELVKLLPKRW VRIGDVLLLP LRPELEPYKH RIAEVYAEVL
GVKTVLRKGH IHGETRKPDY ELLYGSDTVT VHVENGIKYK LDVAKIMFSP ANVKERVRMA
KVAKPDELVV DMFAGIGHLS LPIAVYGKAK VIAIEKDPYT FKFLVENIHL NKVEDRMSAY
NMDNRDFPGE NIADRILMGY VVRTHEFIPK ALSIAKDGAI IHYHNTVPEK LMPREPFETF
KRITKEYGYD VEKLNELKIK RYAPGVWHVV LDLRVFKS
