SYY_METJA
ID SYY_METJA Reviewed; 306 AA.
AC Q57834;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Tyrosine--tRNA ligase;
DE EC=6.1.1.1;
DE AltName: Full=Tyrosyl-tRNA synthetase;
DE Short=TyrRS;
GN Name=tyrS; OrderedLocusNames=MJ0389;
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 FUNCTION, SUBUNIT, AND KINETIC PARAMETERS.
RX PubMed=10585437; DOI=10.1074/jbc.274.50.35601;
RA Steer B.A., Schimmel P.;
RT "Major anticodon-binding region missing from an archaebacterial tRNA
RT synthetase.";
RL J. Biol. Chem. 274:35601-35606(1999).
RN [3]
RP MUTAGENESIS OF ASP-286 AND LYS-288.
RX PubMed=10570126; DOI=10.1073/pnas.96.24.13644;
RA Steer B.A., Schimmel P.;
RT "Domain-domain communication in a miniature archaebacterial tRNA
RT synthetase.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:13644-13649(1999).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEX WITH TRNA(TYR) AND
RP TYROSINE, MUTAGENESIS OF ASP-286, AND SUBUNIT.
RX PubMed=12754495; DOI=10.1038/nsb934;
RA Kobayashi T., Nureki O., Ishitani R., Yaremchuk A., Tukalo M., Cusack S.,
RA Sakamoto K., Yokoyama S.;
RT "Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA
RT synthetases for genetic code expansion.";
RL Nat. Struct. Biol. 10:425-432(2003).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.66 ANGSTROMS) OF WILD-TYPE AND
RP O-METHYL-TYROSINE-SPECIFIC MUTANT APOENZYME.
RX PubMed=15840835; DOI=10.1110/ps.041239305;
RA Zhang Y., Wang L., Schultz P.G., Wilson I.A.;
RT "Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase
RT (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine.";
RL Protein Sci. 14:1340-1349(2005).
CC -!- FUNCTION: Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-
CC step reaction: tyrosine is first activated by ATP to form Tyr-AMP and
CC then transferred to the acceptor end of tRNA(Tyr).
CC {ECO:0000269|PubMed:10585437}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + H(+) + L-
CC tyrosyl-tRNA(Tyr); Xref=Rhea:RHEA:10220, Rhea:RHEA-COMP:9706,
CC Rhea:RHEA-COMP:9707, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:58315, ChEBI:CHEBI:78442,
CC ChEBI:CHEBI:78536, ChEBI:CHEBI:456215; EC=6.1.1.1;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=15 uM for tRNA(Tyr) (at 45 degrees Celsius)
CC {ECO:0000269|PubMed:10585437};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10585437,
CC ECO:0000269|PubMed:12754495}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
CC TyrS type 3 subfamily. {ECO:0000305}.
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DR EMBL; L77117; AAB98375.1; -; Genomic_DNA.
DR PIR; E64348; E64348.
DR RefSeq; WP_010869888.1; NC_000909.1.
DR PDB; 1J1U; X-ray; 1.95 A; A=1-306.
DR PDB; 1U7D; X-ray; 2.65 A; A/B=1-306.
DR PDB; 1U7X; X-ray; 3.00 A; A/B=1-306.
DR PDB; 1ZH0; X-ray; 1.90 A; A=1-306.
DR PDB; 1ZH6; X-ray; 2.50 A; A=1-306.
DR PDB; 2AG6; X-ray; 1.90 A; A=1-306.
DR PDB; 2HGZ; X-ray; 2.50 A; A=2-306.
DR PDB; 2PXH; X-ray; 1.97 A; A=1-306.
DR PDB; 2ZP1; X-ray; 1.70 A; A=1-306.
DR PDB; 3D6U; X-ray; 2.20 A; A=1-306.
DR PDB; 3D6V; X-ray; 2.20 A; A=1-306.
DR PDB; 3N2Y; X-ray; 2.49 A; A/B=1-306.
DR PDB; 3QE4; X-ray; 2.30 A; A/B=1-306.
DR PDB; 4HJR; X-ray; 2.50 A; A/B=1-306.
DR PDB; 4HJX; X-ray; 2.91 A; A/B=1-306.
DR PDB; 4HK4; X-ray; 2.30 A; A=1-306.
DR PDB; 4HPW; X-ray; 2.00 A; A=1-306.
DR PDB; 4ND6; X-ray; 2.00 A; A=1-306.
DR PDB; 4ND7; X-ray; 2.00 A; A=1-306.
DR PDB; 4NDA; X-ray; 1.70 A; A=1-306.
DR PDB; 4NX2; X-ray; 2.00 A; A=1-306.
DR PDB; 4PBR; X-ray; 1.90 A; A=1-306.
DR PDB; 4PBS; X-ray; 2.01 A; A=1-306.
DR PDB; 4PBT; X-ray; 1.90 A; A=1-306.
DR PDB; 5L7P; X-ray; 1.90 A; A/B=1-306.
DR PDB; 5N5U; X-ray; 1.60 A; A=1-306.
DR PDB; 5N5V; X-ray; 2.30 A; A/B/C/D/E/F/G/H=1-306.
DR PDB; 5NSF; X-ray; 2.43 A; A/B/C/D=1-306.
DR PDB; 5U36; X-ray; 3.03 A; A/B=1-306.
DR PDB; 6WRK; X-ray; 1.95 A; A=1-306.
DR PDB; 6WRN; X-ray; 1.60 A; A=1-306.
DR PDB; 6WRQ; X-ray; 1.85 A; A=1-306.
DR PDB; 6WRT; X-ray; 1.55 A; A=1-306.
DR PDB; 7C5C; X-ray; 1.72 A; A=1-306.
DR PDB; 7CKG; X-ray; 2.05 A; A/B=1-306.
DR PDB; 7CKH; X-ray; 1.79 A; A/B=1-306.
DR PDBsum; 1J1U; -.
DR PDBsum; 1U7D; -.
DR PDBsum; 1U7X; -.
DR PDBsum; 1ZH0; -.
DR PDBsum; 1ZH6; -.
DR PDBsum; 2AG6; -.
DR PDBsum; 2HGZ; -.
DR PDBsum; 2PXH; -.
DR PDBsum; 2ZP1; -.
DR PDBsum; 3D6U; -.
DR PDBsum; 3D6V; -.
DR PDBsum; 3N2Y; -.
DR PDBsum; 3QE4; -.
DR PDBsum; 4HJR; -.
DR PDBsum; 4HJX; -.
DR PDBsum; 4HK4; -.
DR PDBsum; 4HPW; -.
DR PDBsum; 4ND6; -.
DR PDBsum; 4ND7; -.
DR PDBsum; 4NDA; -.
DR PDBsum; 4NX2; -.
DR PDBsum; 4PBR; -.
DR PDBsum; 4PBS; -.
DR PDBsum; 4PBT; -.
DR PDBsum; 5L7P; -.
DR PDBsum; 5N5U; -.
DR PDBsum; 5N5V; -.
DR PDBsum; 5NSF; -.
DR PDBsum; 5U36; -.
DR PDBsum; 6WRK; -.
DR PDBsum; 6WRN; -.
DR PDBsum; 6WRQ; -.
DR PDBsum; 6WRT; -.
DR PDBsum; 7C5C; -.
DR PDBsum; 7CKG; -.
DR PDBsum; 7CKH; -.
DR AlphaFoldDB; Q57834; -.
DR SMR; Q57834; -.
DR STRING; 243232.MJ_0389; -.
DR EnsemblBacteria; AAB98375; AAB98375; MJ_0389.
DR GeneID; 1451246; -.
DR KEGG; mja:MJ_0389; -.
DR eggNOG; arCOG01886; Archaea.
DR HOGENOM; CLU_035267_0_1_2; -.
DR InParanoid; Q57834; -.
DR OMA; YIGFEIS; -.
DR OrthoDB; 59062at2157; -.
DR PhylomeDB; Q57834; -.
DR BRENDA; 6.1.1.1; 3260.
DR SABIO-RK; Q57834; -.
DR EvolutionaryTrace; Q57834; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004831; F:tyrosine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006437; P:tyrosyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR CDD; cd00805; TyrRS_core; 1.
DR Gene3D; 3.40.50.620; -; 1.
DR HAMAP; MF_02008; Tyr_tRNA_synth_type3; 1.
DR InterPro; IPR001412; aa-tRNA-synth_I_CS.
DR InterPro; IPR002305; aa-tRNA-synth_Ic.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR InterPro; IPR002307; Tyr-tRNA-ligase.
DR InterPro; IPR023684; Tyr-tRNA-ligase_3.
DR InterPro; IPR023617; Tyr-tRNA-ligase_arc/euk-type.
DR Pfam; PF00579; tRNA-synt_1b; 1.
DR PIRSF; PIRSF006588; TyrRS_arch_euk; 1.
DR PRINTS; PR01040; TRNASYNTHTYR.
DR TIGRFAMs; TIGR00234; tyrS; 1.
DR PROSITE; PS00178; AA_TRNA_LIGASE_I; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW Nucleotide-binding; Protein biosynthesis; Reference proteome.
FT CHAIN 1..306
FT /note="Tyrosine--tRNA ligase"
FT /id="PRO_0000055669"
FT REGION 151..158
FT /note="Tyrosine"
FT REGION 228..231
FT /note="Interaction with t-RNA"
FT REGION 283..288
FT /note="Interaction with t-RNA"
FT MOTIF 37..45
FT /note="'HIGH' region"
FT MOTIF 204..208
FT /note="'KMSKS' region"
FT BINDING 32
FT /ligand="L-tyrosine"
FT /ligand_id="ChEBI:CHEBI:58315"
FT /evidence="ECO:0000269|PubMed:12754495"
FT BINDING 36
FT /ligand="L-tyrosine"
FT /ligand_id="ChEBI:CHEBI:58315"
FT /evidence="ECO:0000269|PubMed:12754495"
FT BINDING 173
FT /ligand="L-tyrosine"
FT /ligand_id="ChEBI:CHEBI:58315"
FT /evidence="ECO:0000269|PubMed:12754495"
FT BINDING 207
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT SITE 143
FT /note="Interaction with t-RNA"
FT MUTAGEN 32
FT /note="Y->Q: Confers specificity for the non-natural amino
FT acid O-methyl-tyrosine; when associated with T-107; A-158
FT and P-162."
FT MUTAGEN 107
FT /note="E->T: Confers specificity for the non-natural amino
FT acid O-methyl-tyrosine; when associated with Q-32; A-158
FT and P-162."
FT MUTAGEN 158
FT /note="D->A: Confers specificity for the non-natural amino
FT acid O-methyl-tyrosine; when associated with Q-32; T-107
FT and P-162."
FT MUTAGEN 162
FT /note="L->P: Confers specificity for the non-natural amino
FT acid O-methyl-tyrosine; when associated with Q-32; T-107
FT and A-158."
FT MUTAGEN 286
FT /note="D->A: Decreases the rate of aminoacylation more than
FT 10-fold, without effect on tyrosyl adenylate synthesis."
FT /evidence="ECO:0000269|PubMed:10570126,
FT ECO:0000269|PubMed:12754495"
FT MUTAGEN 286
FT /note="D->R: Decreases the rate of aminoacylation with
FT wild-type tRNA and increases aminoacylation with amber
FT suppressor tRNA 8-fold. Decreases affinity for wild-type
FT tRNA and increases affinity for amber suppressor tRNA."
FT /evidence="ECO:0000269|PubMed:10570126,
FT ECO:0000269|PubMed:12754495"
FT MUTAGEN 288
FT /note="K->A: Decreases the rate of aminoacylation more than
FT 200-fold, without effect on tyrosyl adenylate synthesis."
FT /evidence="ECO:0000269|PubMed:10570126"
FT HELIX 3..8
FT /evidence="ECO:0007829|PDB:6WRT"
FT STRAND 12..15
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 17..25
FT /evidence="ECO:0007829|PDB:6WRT"
FT STRAND 26..28
FT /evidence="ECO:0007829|PDB:6WRN"
FT STRAND 30..35
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 43..57
FT /evidence="ECO:0007829|PDB:6WRT"
FT STRAND 61..66
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 68..73
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 79..95
FT /evidence="ECO:0007829|PDB:6WRT"
FT STRAND 101..104
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 105..107
FT /evidence="ECO:0007829|PDB:6WRT"
FT TURN 108..110
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 112..124
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 127..133
FT /evidence="ECO:0007829|PDB:6WRT"
FT TURN 134..137
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 146..162
FT /evidence="ECO:0007829|PDB:6WRT"
FT STRAND 165..170
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 171..173
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 174..183
FT /evidence="ECO:0007829|PDB:6WRT"
FT STRAND 184..186
FT /evidence="ECO:0007829|PDB:5N5U"
FT STRAND 189..193
FT /evidence="ECO:0007829|PDB:6WRT"
FT STRAND 201..204
FT /evidence="ECO:0007829|PDB:6WRT"
FT TURN 207..210
FT /evidence="ECO:0007829|PDB:6WRT"
FT STRAND 214..216
FT /evidence="ECO:0007829|PDB:1U7X"
FT HELIX 219..227
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 240..248
FT /evidence="ECO:0007829|PDB:6WRT"
FT STRAND 251..255
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 259..261
FT /evidence="ECO:0007829|PDB:6WRT"
FT STRAND 265..269
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 270..278
FT /evidence="ECO:0007829|PDB:6WRT"
FT HELIX 284..306
FT /evidence="ECO:0007829|PDB:6WRT"
SQ SEQUENCE 306 AA; 35049 MW; 1887760ABAF2DD5E CRC64;
MDEFEMIKRN TSEIISEEEL REVLKKDEKS AYIGFEPSGK IHLGHYLQIK KMIDLQNAGF
DIIILLADLH AYLNQKGELD EIRKIGDYNK KVFEAMGLKA KYVYGSEFQL DKDYTLNVYR
LALKTTLKRA RRSMELIARE DENPKVAEVI YPIMQVNDIH YLGVDVAVGG MEQRKIHMLA
RELLPKKVVC IHNPVLTGLD GEGKMSSSKG NFIAVDDSPE EIRAKIKKAY CPAGVVEGNP
IMEIAKYFLE YPLTIKRPEK FGGDLTVNSY EELESLFKNK ELHPMDLKNA VAEELIKILE
PIRKRL
