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Protein

Lysine--tRNA ligase

Gene

lysS

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).

Cofactori

Zn2+Note: Binds 2 Zn2+ ions per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi95 – 951Zinc 1
Metal bindingi99 – 991Zinc 1
Metal bindingi100 – 1001Zinc 1
Metal bindingi106 – 1061Zinc 1
Metal bindingi177 – 1771Zinc 2
Metal bindingi180 – 1801Zinc 2
Metal bindingi199 – 1991Zinc 2
Metal bindingi203 – 2031Zinc 2

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Aminoacyl-tRNA synthetase, Ligase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-215-MONOMER.
BRENDAi6.1.1.6. 5244.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine--tRNA ligase (EC:6.1.1.6)
Alternative name(s):
Lysyl-tRNA synthetase
Short name:
LysRS
Gene namesi
Name:lysS
Ordered Locus Names:PH0224
OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Taxonomic identifieri70601 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000000752 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 523523Lysine--tRNA ligasePRO_0000152760Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi70601.PH0224.

Structurei

Secondary structure

1
523
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 1512Combined sources
Beta strandi20 – 289Combined sources
Helixi36 – 5318Combined sources
Turni54 – 563Combined sources
Beta strandi58 – 658Combined sources
Beta strandi76 – 783Combined sources
Helixi80 – 856Combined sources
Turni90 – 923Combined sources
Beta strandi98 – 1025Combined sources
Helixi103 – 11614Combined sources
Turni117 – 1193Combined sources
Beta strandi123 – 1264Combined sources
Helixi127 – 1326Combined sources
Turni133 – 1364Combined sources
Helixi137 – 1459Combined sources
Helixi147 – 16014Combined sources
Beta strandi172 – 1765Combined sources
Turni178 – 1803Combined sources
Beta strandi186 – 1894Combined sources
Beta strandi191 – 1933Combined sources
Beta strandi195 – 1973Combined sources
Beta strandi200 – 2023Combined sources
Beta strandi214 – 2163Combined sources
Helixi218 – 22811Combined sources
Helixi238 – 2414Combined sources
Helixi246 – 25813Combined sources
Beta strandi271 – 2744Combined sources
Helixi290 – 2945Combined sources
Helixi299 – 3079Combined sources
Beta strandi315 – 3173Combined sources
Helixi323 – 33715Combined sources
Helixi349 – 3579Combined sources
Helixi371 – 3777Combined sources
Helixi385 – 39410Combined sources
Helixi404 – 42320Combined sources
Helixi427 – 4293Combined sources
Helixi444 – 45815Combined sources
Helixi465 – 47915Combined sources
Helixi483 – 49513Combined sources
Beta strandi496 – 4994Combined sources
Helixi503 – 5086Combined sources
Helixi512 – 5198Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IRXX-ray2.60A/B1-523[»]
ProteinModelPortaliO57963.
SMRiO57963. Positions 3-523.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO57963.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi30 – 389"HIGH" region
Motifi279 – 2835"KMSKS" region

Sequence similaritiesi

Phylogenomic databases

eggNOGiarCOG00485. Archaea.
COG1384. LUCA.
HOGENOMiHOG000226938.
KOiK04566.
OMAiHNNAMLR.

Family and domain databases

Gene3Di1.10.10.350. 1 hit.
2.30.30.300. 1 hit.
3.40.50.620. 2 hits.
HAMAPiMF_00177. Lys_tRNA_synth_class1. 1 hit.
InterProiIPR008925. aa-tRNA-synth_I_codon-bd.
IPR020751. aa-tRNA-synth_I_codon-bd_sub2.
IPR001412. aa-tRNA-synth_I_CS.
IPR002904. Lys-tRNA-ligase.
IPR023386. Lys-tRNA-ligase_insertion.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
SUPFAMiSSF48163. SSF48163. 1 hit.
TIGRFAMsiTIGR00467. lysS_arch. 1 hit.
PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O57963-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVHWADYIAD KIIRERGEKE KYVVESGITP SGYVHVGNFR ELFTAYIVGH
60 70 80 90 100
ALRDKGYEVR HIHMWDDYDR FRKVPRNVPQ EWKDYLGMPI SEVPDPWGCH
110 120 130 140 150
ESYAEHFMRK FEEEVEKLGI EVDFLYASEL YKRGEYSEEI RLAFEKRDKI
160 170 180 190 200
MEILNKYREI AKQPPLPENW WPAMVYCPEH RREAEIIEWD GGWKVKYKCP
210 220 230 240 250
EGHEGWVDIR SGNVKLRWRV DWPMRWSHFG VDFEPAGKDH LVAGSSYDTG
260 270 280 290 300
KEIIKEVYGK EAPLSLMYEF VGIKGQKGKM SGSKGNVILL SDLYEVLEPG
310 320 330 340 350
LVRFIYARHR PNKEIKIDLG LGILNLYDEF DKVERIYFGV EGGKGDDEEL
360 370 380 390 400
RRTYELSMPK KPERLVAQAP FRFLAVLVQL PHLTEEDIIN VLIKQGHIPR
410 420 430 440 450
DLSKEDVERV KLRINLARNW VKKYAPEDVK FSILEKPPEV EVSEDVREAM
460 470 480 490 500
NEVAEWLENH EEFSVEEFNN ILFEVAKRRG ISSREWFSTL YRLFIGKERG
510 520
PRLASFLASL DRSFVIKRLR LEG
Length:523
Mass (Da):61,579
Last modified:August 1, 1998 - v1
Checksum:i0FA9AD39FE7FCD49
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29296.1.
PIRiA71246.
RefSeqiWP_010884327.1. NC_000961.1.

Genome annotation databases

EnsemblBacteriaiBAA29296; BAA29296; BAA29296.
GeneIDi1444114.
KEGGipho:PH0224.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000001 Genomic DNA. Translation: BAA29296.1.
PIRiA71246.
RefSeqiWP_010884327.1. NC_000961.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IRXX-ray2.60A/B1-523[»]
ProteinModelPortaliO57963.
SMRiO57963. Positions 3-523.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi70601.PH0224.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA29296; BAA29296; BAA29296.
GeneIDi1444114.
KEGGipho:PH0224.

Phylogenomic databases

eggNOGiarCOG00485. Archaea.
COG1384. LUCA.
HOGENOMiHOG000226938.
KOiK04566.
OMAiHNNAMLR.

Enzyme and pathway databases

BioCyciPHOR70601:GJWR-215-MONOMER.
BRENDAi6.1.1.6. 5244.

Miscellaneous databases

EvolutionaryTraceiO57963.

Family and domain databases

Gene3Di1.10.10.350. 1 hit.
2.30.30.300. 1 hit.
3.40.50.620. 2 hits.
HAMAPiMF_00177. Lys_tRNA_synth_class1. 1 hit.
InterProiIPR008925. aa-tRNA-synth_I_codon-bd.
IPR020751. aa-tRNA-synth_I_codon-bd_sub2.
IPR001412. aa-tRNA-synth_I_CS.
IPR002904. Lys-tRNA-ligase.
IPR023386. Lys-tRNA-ligase_insertion.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
SUPFAMiSSF48163. SSF48163. 1 hit.
TIGRFAMsiTIGR00467. lysS_arch. 1 hit.
PROSITEiPS00178. AA_TRNA_LIGASE_I. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSYK_PYRHO
AccessioniPrimary (citable) accession number: O57963
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: August 1, 1998
Last modified: November 11, 2015
This is version 113 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. Aminoacyl-tRNA synthetases
    List of aminoacyl-tRNA synthetase entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.