SYM_PYRAB
ID SYM_PYRAB Reviewed; 722 AA.
AC Q9V011; G8ZIF2;
DT 20-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 158.
DE RecName: Full=Methionine--tRNA ligase {ECO:0000255|HAMAP-Rule:MF_00098};
DE EC=6.1.1.10 {ECO:0000255|HAMAP-Rule:MF_00098};
DE AltName: Full=Methionyl-tRNA synthetase {ECO:0000255|HAMAP-Rule:MF_00098};
DE Short=MetRS {ECO:0000255|HAMAP-Rule:MF_00098};
GN Name=metG {ECO:0000255|HAMAP-Rule:MF_00098}; Synonyms=metS;
GN OrderedLocusNames=PYRAB09870; ORFNames=PAB2364;
OS Pyrococcus abyssi (strain GE5 / Orsay).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=272844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GE5 / Orsay;
RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA Weissenbach J., Zivanovic Y., Forterre P.;
RT "An integrated analysis of the genome of the hyperthermophilic archaeon
RT Pyrococcus abyssi.";
RL Mol. Microbiol. 47:1495-1512(2003).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=GE5 / Orsay;
RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA Gao J., Wang J.;
RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT Pyrococcus furiosus DSM 3638.";
RL Curr. Microbiol. 64:118-129(2012).
CC -!- FUNCTION: Is required not only for elongation of protein synthesis but
CC also for the initiation of all mRNA translation through initiator
CC tRNA(fMet) aminoacylation. {ECO:0000255|HAMAP-Rule:MF_00098}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-
CC methionyl-tRNA(Met); Xref=Rhea:RHEA:13481, Rhea:RHEA-COMP:9667,
CC Rhea:RHEA-COMP:9698, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:78442, ChEBI:CHEBI:78530,
CC ChEBI:CHEBI:456215; EC=6.1.1.10; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00098};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00098};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00098};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00098}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00098}.
CC -!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
CC MetG type 1 subfamily. {ECO:0000255|HAMAP-Rule:MF_00098}.
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DR EMBL; AJ248286; CAB49895.1; -; Genomic_DNA.
DR EMBL; HE613800; CCE70393.1; -; Genomic_DNA.
DR PIR; B75074; B75074.
DR RefSeq; WP_010868104.1; NC_000868.1.
DR PDB; 1MKH; X-ray; 2.01 A; A=616-722.
DR PDB; 1RQG; X-ray; 2.90 A; A=1-722.
DR PDBsum; 1MKH; -.
DR PDBsum; 1RQG; -.
DR AlphaFoldDB; Q9V011; -.
DR SMR; Q9V011; -.
DR STRING; 272844.PAB2364; -.
DR EnsemblBacteria; CAB49895; CAB49895; PAB2364.
DR GeneID; 1496337; -.
DR KEGG; pab:PAB2364; -.
DR PATRIC; fig|272844.11.peg.1039; -.
DR eggNOG; arCOG00810; Archaea.
DR HOGENOM; CLU_009710_1_2_2; -.
DR OMA; SDMHGTP; -.
DR OrthoDB; 6590at2157; -.
DR PhylomeDB; Q9V011; -.
DR BRENDA; 6.1.1.10; 5242.
DR EvolutionaryTrace; Q9V011; -.
DR Proteomes; UP000000810; Chromosome.
DR Proteomes; UP000009139; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004825; F:methionine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006431; P:methionyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR CDD; cd07957; Anticodon_Ia_Met; 1.
DR CDD; cd00814; MetRS_core; 1.
DR Gene3D; 2.20.28.20; -; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.620; -; 1.
DR HAMAP; MF_00098; Met_tRNA_synth_type1; 1.
DR InterPro; IPR001412; aa-tRNA-synth_I_CS.
DR InterPro; IPR041872; Anticodon_Met.
DR InterPro; IPR004495; Met-tRNA-synth_bsu_C.
DR InterPro; IPR023458; Met-tRNA_ligase_1.
DR InterPro; IPR014758; Met-tRNA_synth.
DR InterPro; IPR015413; Methionyl/Leucyl_tRNA_Synth.
DR InterPro; IPR033911; MetRS_core.
DR InterPro; IPR029038; MetRS_Zn.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR InterPro; IPR002547; tRNA-bd_dom.
DR InterPro; IPR009080; tRNAsynth_Ia_anticodon-bd.
DR PANTHER; PTHR45765; PTHR45765; 1.
DR Pfam; PF19303; Anticodon_3; 1.
DR Pfam; PF09334; tRNA-synt_1g; 1.
DR Pfam; PF01588; tRNA_bind; 1.
DR PRINTS; PR01041; TRNASYNTHMET.
DR SUPFAM; SSF47323; SSF47323; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF57770; SSF57770; 1.
DR TIGRFAMs; TIGR00398; metG; 1.
DR TIGRFAMs; TIGR00399; metG_C_term; 1.
DR PROSITE; PS00178; AA_TRNA_LIGASE_I; 1.
DR PROSITE; PS50886; TRBD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminoacyl-tRNA synthetase; ATP-binding; Cytoplasm; Ligase;
KW Metal-binding; Nucleotide-binding; Protein biosynthesis; RNA-binding;
KW tRNA-binding; Zinc.
FT CHAIN 1..722
FT /note="Methionine--tRNA ligase"
FT /id="PRO_0000139194"
FT DOMAIN 622..722
FT /note="tRNA-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00098"
FT MOTIF 11..21
FT /note="'HIGH' region"
FT MOTIF 344..348
FT /note="'KMSKS' region"
FT BINDING 143
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00098"
FT BINDING 146
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00098"
FT BINDING 156
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00098"
FT BINDING 159
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00098"
FT BINDING 347
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00098"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 19..25
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 27..38
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 42..50
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 54..63
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 67..85
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 90..94
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 98..113
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 117..127
FT /evidence="ECO:0007829|PDB:1RQG"
FT TURN 128..131
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 136..138
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:1RQG"
FT TURN 153..155
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 157..159
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 167..170
FT /evidence="ECO:0007829|PDB:1RQG"
FT TURN 174..176
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 181..190
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 192..194
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 196..204
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 210..220
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 234..236
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 244..246
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 253..256
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 257..259
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 260..271
FT /evidence="ECO:0007829|PDB:1RQG"
FT TURN 275..278
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 279..282
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 289..296
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 297..299
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 300..304
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 306..312
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 319..321
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 338..340
FT /evidence="ECO:0007829|PDB:1RQG"
FT TURN 347..350
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 355..358
FT /evidence="ECO:0007829|PDB:1RQG"
FT TURN 359..361
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 364..373
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 377..379
FT /evidence="ECO:0007829|PDB:1RQG"
FT STRAND 381..383
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 385..394
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 395..399
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 400..413
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 427..448
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 452..471
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 475..478
FT /evidence="ECO:0007829|PDB:1RQG"
FT TURN 479..481
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 483..504
FT /evidence="ECO:0007829|PDB:1RQG"
FT TURN 505..507
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 509..518
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 550..559
FT /evidence="ECO:0007829|PDB:1RQG"
FT TURN 560..564
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 566..576
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 579..590
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 591..594
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 595..601
FT /evidence="ECO:0007829|PDB:1RQG"
FT HELIX 620..624
FT /evidence="ECO:0007829|PDB:1MKH"
FT STRAND 628..638
FT /evidence="ECO:0007829|PDB:1MKH"
FT STRAND 646..651
FT /evidence="ECO:0007829|PDB:1MKH"
FT STRAND 656..661
FT /evidence="ECO:0007829|PDB:1MKH"
FT TURN 664..666
FT /evidence="ECO:0007829|PDB:1MKH"
FT HELIX 669..672
FT /evidence="ECO:0007829|PDB:1MKH"
FT STRAND 676..680
FT /evidence="ECO:0007829|PDB:1MKH"
FT STRAND 699..701
FT /evidence="ECO:0007829|PDB:1MKH"
FT STRAND 706..708
FT /evidence="ECO:0007829|PDB:1MKH"
SQ SEQUENCE 722 AA; 84295 MW; A69078A91D5BE028 CRC64;
MVRYMVTSAL PYANGPIHAG HLAGAYLPAD IFVRYLRLKG EDVVFICGTD EHGTPISFRA
LKEGRSPREI VDEFHEQIKI TFQRAKISFD FFGRTELPIH YKLSQEFFLK AYENGHLVKK
VTKQAYCEHD KMFLPDRFVI GTCPYCGAED QKGDQCEVCG RPLTPEILIN PRCAICGRPI
SFRDSAHYYI KMQDFAERLK RWIEKQPWKP NVKNMVLSWI EEGLEERAIT RDLNWGIPVP
LDEEDMKGKV LYVWFEAPIG YISITIEHFK RIGKPNEWKK YWLNIDGQTR VIHFIGKDNI
PFHAIFWPAF LMAYGKYKDE EVEAEWNLPY DIPANEYLTL EGKKFSTSRN WAIWVHEFLD
VFPADYLRYY LTTIMPETRD SDFSFSDFKV RINEELVNNL GNFVHRALTF VNRYFDGVVP
ERGELDELDR EALEEIEKAF KEVGELIMNY RFKDALKRVM SLASFGNRYF DHKQPWKTAK
EDKVRTGTTV NISLQIVKAL GILLEPFLPD ASEKIWHLLN LDEVKRWEFR ELPAGHKVRK
PEILFKKVTD DQIIYFILNY MAKGNPEGAR ILLDKYYKRE DVIRVAKEKF GDEAEVVLRR
VYKDIKLKEK KEGKEMYVKF DDFAKLDLRV GKIIEVKDHP NADKLYVVKV DLGDEVRTLV
AGLKKYYKPE ELLNRYVVVV ANLEPKKLRG IGSQGMLLAA DDGERVALLM PDKEVKLGAK
VR
