SYK_PYRHO
ID SYK_PYRHO Reviewed; 523 AA.
AC O57963;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Lysine--tRNA ligase;
DE EC=6.1.1.6;
DE AltName: Full=Lysyl-tRNA synthetase;
DE Short=LysRS;
GN Name=lysS; OrderedLocusNames=PH0224;
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 X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
RX PubMed=11887185; DOI=10.1038/nsb777;
RA Terada T., Nureki O., Ishitani R., Ambrogelly A., Ibba M., Soell D.,
RA Yokoyama S.;
RT "Functional convergence of two lysyl-tRNA synthetases with unrelated
RT topologies.";
RL Nat. Struct. Biol. 9:257-262(2002).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-
CC tRNA(Lys); Xref=Rhea:RHEA:20792, Rhea:RHEA-COMP:9696, Rhea:RHEA-
CC COMP:9697, ChEBI:CHEBI:30616, ChEBI:CHEBI:32551, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:78442, ChEBI:CHEBI:78529, ChEBI:CHEBI:456215; EC=6.1.1.6;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Note=Binds 2 Zn(2+) ions per subunit.;
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the class-I aminoacyl-tRNA synthetase family.
CC {ECO:0000305}.
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DR EMBL; BA000001; BAA29296.1; -; Genomic_DNA.
DR PIR; A71246; A71246.
DR RefSeq; WP_010884327.1; NC_000961.1.
DR PDB; 1IRX; X-ray; 2.60 A; A/B=1-523.
DR PDBsum; 1IRX; -.
DR AlphaFoldDB; O57963; -.
DR SMR; O57963; -.
DR STRING; 70601.3256613; -.
DR EnsemblBacteria; BAA29296; BAA29296; BAA29296.
DR GeneID; 1444114; -.
DR KEGG; pho:PH0224; -.
DR eggNOG; arCOG00485; Archaea.
DR OMA; DWPMRWA; -.
DR OrthoDB; 9880at2157; -.
DR BRENDA; 6.1.1.6; 5244.
DR EvolutionaryTrace; O57963; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004824; F:lysine-tRNA ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000049; F:tRNA binding; IEA:InterPro.
DR GO; GO:0006430; P:lysyl-tRNA aminoacylation; IEA:UniProtKB-UniRule.
DR Gene3D; 1.10.10.350; -; 1.
DR Gene3D; 3.40.50.620; -; 2.
DR Gene3D; 6.10.20.10; -; 1.
DR HAMAP; MF_00177; Lys_tRNA_synth_class1; 1.
DR InterPro; IPR045462; aa-tRNA-synth_I_cd-bd.
DR InterPro; IPR020751; aa-tRNA-synth_I_codon-bd_sub2.
DR InterPro; IPR001412; aa-tRNA-synth_I_CS.
DR InterPro; IPR008925; aa_tRNA-synth_I_cd-bd_sf.
DR InterPro; IPR002904; Lys-tRNA-ligase.
DR InterPro; IPR042078; Lys-tRNA-ligase_SC_fold.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR PANTHER; PTHR37940; PTHR37940; 1.
DR Pfam; PF19269; Anticodon_2; 1.
DR Pfam; PF01921; tRNA-synt_1f; 1.
DR SUPFAM; SSF48163; SSF48163; 1.
DR TIGRFAMs; TIGR00467; lysS_arch; 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 Metal-binding; Nucleotide-binding; Protein biosynthesis; Zinc.
FT CHAIN 1..523
FT /note="Lysine--tRNA ligase"
FT /id="PRO_0000152760"
FT MOTIF 30..38
FT /note="'HIGH' region"
FT MOTIF 279..283
FT /note="'KMSKS' region"
FT BINDING 95
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 100
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 106
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT BINDING 177
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 180
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 199
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT BINDING 203
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT HELIX 4..15
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 20..28
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 36..53
FT /evidence="ECO:0007829|PDB:1IRX"
FT TURN 54..56
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 58..65
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 80..85
FT /evidence="ECO:0007829|PDB:1IRX"
FT TURN 90..92
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 98..102
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 103..116
FT /evidence="ECO:0007829|PDB:1IRX"
FT TURN 117..119
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 123..126
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 127..132
FT /evidence="ECO:0007829|PDB:1IRX"
FT TURN 133..136
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 137..145
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 147..160
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 172..176
FT /evidence="ECO:0007829|PDB:1IRX"
FT TURN 178..180
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 186..189
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 191..193
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 195..197
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 200..202
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 214..216
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 218..228
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 238..241
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 246..258
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 271..274
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 290..294
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 299..307
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 315..317
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 323..337
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 349..357
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 371..377
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 385..394
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 404..423
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 427..429
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 444..458
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 465..479
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 483..495
FT /evidence="ECO:0007829|PDB:1IRX"
FT STRAND 496..499
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 503..508
FT /evidence="ECO:0007829|PDB:1IRX"
FT HELIX 512..519
FT /evidence="ECO:0007829|PDB:1IRX"
SQ SEQUENCE 523 AA; 61579 MW; 0FA9AD39FE7FCD49 CRC64;
MVHWADYIAD KIIRERGEKE KYVVESGITP SGYVHVGNFR ELFTAYIVGH ALRDKGYEVR
HIHMWDDYDR FRKVPRNVPQ EWKDYLGMPI SEVPDPWGCH ESYAEHFMRK FEEEVEKLGI
EVDFLYASEL YKRGEYSEEI RLAFEKRDKI MEILNKYREI AKQPPLPENW WPAMVYCPEH
RREAEIIEWD GGWKVKYKCP EGHEGWVDIR SGNVKLRWRV DWPMRWSHFG VDFEPAGKDH
LVAGSSYDTG KEIIKEVYGK EAPLSLMYEF VGIKGQKGKM SGSKGNVILL SDLYEVLEPG
LVRFIYARHR PNKEIKIDLG LGILNLYDEF DKVERIYFGV EGGKGDDEEL RRTYELSMPK
KPERLVAQAP FRFLAVLVQL PHLTEEDIIN VLIKQGHIPR DLSKEDVERV KLRINLARNW
VKKYAPEDVK FSILEKPPEV EVSEDVREAM NEVAEWLENH EEFSVEEFNN ILFEVAKRRG
ISSREWFSTL YRLFIGKERG PRLASFLASL DRSFVIKRLR LEG
