Q6YR34 (SYI_ONYPE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Isoleucine--tRNA ligase
EC=6.1.1.5

Alternative name(s):
Isoleucyl-tRNA synthetase
Short name=IleRS

Gene names

Name:	ileS
Ordered Locus Names:	PAM_184

Organism

Onion yellows phytoplasma (strain OY-M) [Complete proteome] [HAMAP]

Taxonomic identifier

262768 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Tenericutes › Mollicutes › Acholeplasmatales › Acholeplasmataceae › Candidatus Phytoplasma › Candidatus Phytoplasma asteris › Onion yellows phytoplasma

Protein attributes

Sequence length	900 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) By similarity. HAMAP-Rule MF_02002
Catalytic activity	ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile). HAMAP-Rule MF_02002
Cofactor	Binds 1 zinc ion per subunit By similarity.
Subunit structure	Monomer By similarity.
Subcellular location	Cytoplasm By similarity.
Domain	IleRS has two distinct active sites: one for aminoacylation and one for editing. The misactivated valine is translocated from the active site to the editing site, which sterically excludes the correctly activated isoleucine. The single editing site contains two valyl binding pockets, one specific for each substrate (Val-AMP or Val-tRNA(Ile)) By similarity. HAMAP-Rule MF_02002
Sequence similarities	Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily.

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Aminoacyl-tRNA synthetase Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	isoleucyl-tRNA aminoacylation Inferred from electronic annotation. Source: HAMAP regulation of translational fidelity Inferred from electronic annotation. Source: GOC
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP aminoacyl-tRNA editing activity Inferred from electronic annotation. Source: InterPro isoleucine-tRNA ligase activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 900	900	Isoleucine--tRNA ligase HAMAP-Rule MF_02002		PRO_0000098433
Regions
	Motif	59 – 69	11	"HIGH" region HAMAP-Rule MF_02002
	Motif	591 – 595	5	"KMSKS" region HAMAP-Rule MF_02002
Sites
	Metal binding	876	1	Zinc By similarity
	Metal binding	879	1	Zinc By similarity
	Metal binding	892	1	Zinc By similarity
	Metal binding	895	1	Zinc By similarity
	Binding site	550	1	Aminoacyl-adenylate By similarity
	Binding site	594	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q6YR34 [UniParc]. Last modified July 5, 2004. Version 1. Checksum: 023BA5BF424BF031	FASTA	900	104,373
	10 20 30 40 50 60 MTTNYKTTLL MPKTDFPMKG NLGKNEINIQ KHWQKLDLYQ KKLQQNQDNN PFILHDGPPY 70 80 90 100 110 120 ANGNIHMGHA LNKILKDFIV RFRSMQGFYT PLIPGWDTHG LPIEAAVLKK TSKNAFTRKP 130 140 150 160 170 180 LLDKCQEFAL ENVNNQKHQF QRLGILGDWQ NPYLTLDKTF VSDQVRIFGQ MVDKGLIFKA 190 200 210 220 230 240 LKPIHWSPTL ESALAEAELE YHNHQSPSVY VAFSMKKLDI FDNVALVIWT TTPWTLPANV 250 260 270 280 290 300 AIAVHPEKEY QLIEVLQKRY LVGTKNIPFL QKVFAWNKEN IKVVATFEGK TLEHLTYQNH 310 320 330 340 350 360 LVSKFGKIIL SQHVLDGEGT GLVHIAPGHG LDDFLVGQKY NLDVVCSIDK KGMMTDVSKY 370 380 390 400 410 420 QGLFYTKANE AIISDLEKDH SLLKADVILH SYPHDWRTKK PVISLALPQW FVSIKKIKSL 430 440 450 460 470 480 LLEETQKVKW IPRWGELKMT NMITNREDWN ISRQRTWGVP IPIFYTETHQ PILDLKLINH 490 500 510 520 530 540 VADLFEQHGM DIWYEWDVKK LLPENYINPQ SPNNLFTKEL DIMDVWFDSG TSYSVFKKRN 550 560 570 580 590 600 QVLQSDVYLE GSDQYRGWFN SSLITSVATQ NQAPYKTVIT HGFVFDGEGK KMSKSLGNVI 610 620 630 640 650 660 DPLTVAEQKG ADIIRLWVAN TNYNLDVRIN PSILKQVEDL YRKIRNTFRF MLGNLDNFKK 670 680 690 700 710 720 DTNYIAFEQR TFIHQAMMLD FEEVLKNVLH SYDTYNFEGV LRHLFPFITN KISAFYLDFA 730 740 750 760 770 780 KDILYIEKED HKERKMIQST IYDLLLSLLQ VLTPIIPHTT SEVYGFFPFA VEKDIYLEKM 790 800 810 820 830 840 PQLKARPTSH LLLEYHKFLT LRKNVLQYLE KARQSGLINS SLQAHITLSL TQEEMHALDV 850 860 870 880 890 900 LQIKDQLHQL FIVSKVTLQL KDTFDVKVAK ASGYACQRCW NVVITKPLTP LCTRCQNILK

References

[1]

"Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma." Oshima K., Kakizawa S., Nishigawa H., Jung H.-Y., Wei W., Suzuki S., Arashida R., Nakata D., Miyata S., Ugaki M., Namba S. Nat. Genet. 36:27-29(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: OY-M.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AP006628 Genomic DNA. Translation: BAD04269.1.
RefSeq	NP_950436.1. NC_005303.2.
3D structure databases
ProteinModelPortal	Q6YR34.
ModBase	Search...
Protein-protein interaction databases
STRING	262768.PAM_184.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAD04269; BAD04269; PAM_184.
GeneID	2673552.
KEGG	poy:PAM_184.
PATRIC	22809860. VBIOniYel86799_0253.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0060.
HOGENOM	HOG000246402.
KO	K01870.
OMA	KQVLTHG.
ProtClustDB	PRK05743.
Enzyme and pathway databases
BioCyc	MORG262768:GHF5-196-MONOMER.
Family and domain databases
Gene3D	3.40.50.620. 2 hits. 3.90.740.10. 1 hit.
HAMAP	MF_02002. Ile_tRNA_synth_type1.
InterPro	IPR001412. aa-tRNA-synth_I_CS. IPR002300. aa-tRNA-synth_Ia. IPR002301. Ile-tRNA-ligase. IPR023585. Ile-tRNA-ligase_type1. IPR014729. Rossmann-like_a/b/a_fold. IPR009080. tRNAsynth_1a_anticodon-bd. IPR013155. V/L/I-tRNA-synth_anticodon-bd. IPR009008. Val/Leu/Ile-tRNA-synth_edit. IPR010663. Znf_DNA_glyclase/IsotRNA_synth. [Graphical view]
PANTHER	PTHR11946:SF9. PTHR11946:SF9. 1 hit.
Pfam	PF08264. Anticodon_1. 1 hit. PF00133. tRNA-synt_1. 1 hit. PF06827. zf-FPG_IleRS. 1 hit. [Graphical view]
PRINTS	PR00984. TRNASYNTHILE.
SUPFAM	SSF47323. tRNAsyn_1a_bind. 1 hit. SSF50677. ValRS_IleRS_edit. 1 hit.
TIGRFAMs	TIGR00392. ileS. 1 hit.
PROSITE	PS00178. AA_TRNA_LIGASE_I. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

SYI_ONYPE

Accession

Primary (citable) accession number: Q6YR34

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 20, 2005
Last sequence update:	July 5, 2004
Last modified:	May 1, 2013
This is version 68 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program