Reviewed, UniProtKB/Swiss-Prot Q83JU6 (SYK1_SHIFL)

Names and origin

Protein names

Recommended name:
    Lysyl-tRNA synthetase
    EC=6.1.1.6
Alternative name(s):
    Lysine--tRNA ligase
      Short name=LysRS

Gene names

Name:	lysS
Ordered Locus Names:	SF2876, S3075

Organism

Shigella flexneri [Complete proteome] [HAMAP]

Taxonomic identifier

623 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Shigella

Protein attributes

Sequence length	505 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Inferred from homology.

General annotation (Comments)

Catalytic activity	ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys). HAMAP MF_00252
Cofactor	Binds 3 magnesium ions per subunit By similarity.
Subunit structure	Homodimer By similarity.
Subcellular location	Cytoplasm. HAMAP MF_00252
Sequence similarities	Belongs to the class-II aminoacyl-tRNA synthetase family.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	lysyl-tRNA aminoacylation Inferred from electronic annotation. Source: HAMAP
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP lysine-tRNA ligase activity Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from electronic annotation. Source: HAMAP nucleic acid binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed By similarity
	Chain	2 – 505	504	Lysyl-tRNA synthetase HAMAP MF_00252		PRO_0000152674
Sites
	Metal binding	415	1	Magnesium 1 By similarity
	Metal binding	422	1	Magnesium 1 By similarity
	Metal binding	422	1	Magnesium 2 By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q83JU6-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 28FB030C11E077D4	FASTA	505	57,617
	10 20 30 40 50 60 MSEQHAQGAD AVVDLNNELK TRREKLANLR EQGIAFPNDF RRDHTSDQLH AEFDGKENEE 70 80 90 100 110 120 LEALNIEVAV AGRMMTRRIM GKASFVTLQD VGGRIQLYVA RDDLPEGVYN EQFKKWDLGD 130 140 150 160 170 180 ILGAKGKLFK TKTGELSIHC TELRLLTKAL RPLPDKFHGL QDQEARYRQR YLDLISNDES 190 200 210 220 230 240 RNTFKVRSQI LSGIRQFMVN RGFMEVETPM MQVIPGGAAA RPFITHHNAL DLDMYLRIAP 250 260 270 280 290 300 ELYLKRLVVG GFERVFEINR NFRNEGISVR HNPEFTMMEL YMAYADYKDL IELTESLFRT 310 320 330 340 350 360 LAQDILGKTE VTYGDVTLDF GKPFEKLTMR EAIKKYRPET DMADLDNFDS AKAIAESIGI 370 380 390 400 410 420 HVEKSWGLGR IVTEIFEEVA EAHLIQPTFI TEYPAEVSPL ARRNDINPEI TDRFEFFIGG 430 440 450 460 470 480 REIGNGFSEL NDAEDQAQRF LDQVAAKDAG DDEAMFYDED YVTALEHGLP PTAGLGIGID 490 500 RMVMLFTNSH TIRDVILFPA MRPVK

References

[1]

"Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157." Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y. , Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J. Nucleic Acids Res. 30:4432-4441(2002) [PubMed: 12384590] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 301 / Serotype 2a.

[2]

"Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T." Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W., Fournier G., Mayhew G.F., Plunkett G. III, Rose D.J., Darling A., Mau B., Perna N.T., Payne S.M., Runyen-Janecky L.J., Zhou S., Schwartz D.C., Blattner F.R. Infect. Immun. 71:2775-2786(2003) [PubMed: 12704152] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700930 / 2457T / Serotype 2a.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AE005674 Genomic DNA. Translation: AAN44362.1. AE014073 Genomic DNA. Translation: AAP18183.1.
RefSeq	NP_708655.1. NP_838373.1.
3D structure databases
HSSP	HSSP built from PDB template 1KRS based on UniProtKB P13030.
SMR	Q83JU6. Positions 13-503.
ModBase	Search...
Genome annotation databases
GeneID	1025848. 1079763.
GenomeReviews	Gene locus SF2876 in contig AE005674_GR. Gene locus S3075 in contig AE014073_GR.
KEGG	sfl:SF2876. sfx:S3075.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q83JU6.
OMA	QMMSPLA.
Enzyme and pathway databases
BioCyc	SFLE198214:AAN44362.1-MON.
BRENDA	6.1.1.6. 189495.
Family and domain databases
HAMAP	MF_00252. [Tree]
InterPro	IPR004364. aa-tRNA-synt_II. IPR018150. aa-tRNA-synt_II-like. IPR006195. aa-tRNA-synth_II_cons-reg. IPR002313. Lys-tRNA-synth_II. IPR018149. Lys-tRNA-synth_II_C. IPR012340. NA-bd_OB-fold. IPR004365. NA_bd_OB_tRNA-helicase. [Graphical view]
Gene3D	G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
PANTHER	PTHR22594. aa-tRNA-synt_II. 1 hit. PTHR22594:SF4. tRNA-synt_lys_2. 1 hit.
Pfam	PF00152. tRNA-synt_2. 1 hit. PF01336. tRNA_anti. 1 hit. [Graphical view]
PRINTS	PR00982. TRNASYNTHLYS.
TIGRFAMs	TIGR00499. lysS_bact. 1 hit.
PROSITE	PS50862. AA_TRNA_LIGASE_II. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

SYK1_SHIFL

Accession

Primary (citable) accession number: Q83JU6

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 2003
Last sequence update:	January 23, 2007
Last modified:	November 3, 2009
This is version 51 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)