P18330 (SYI1_PSEFL) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Isoleucine--tRNA ligase 1
EC=6.1.1.5

Alternative name(s):
Isoleucyl-tRNA synthetase 1
Short name=IleRS 1

Gene names

Name:	ileS1
Synonyms:	ileS

Organism

Pseudomonas fluorescens

Taxonomic identifier

294 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas › Pseudomonas fluorescens group

Protein attributes

Sequence length	943 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 Confers resistance to the antibiotic mupirocin (pseudomonic acid A), an Ile-analog produced by P.fluorescens NCIMB 10586 itself that competitively inhibits activation by Ile-tRNA synthetase, thus inhibiting protein biosynthesis. 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.
Subcellular location	Cytoplasm HAMAP-Rule MF_02002.
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
Miscellaneous	P.fluorescens NCIMB 10586 possesses two distinct IleRSs (IleRS-R1 and IleRS-R2), each with a different level of sensitivity to mupirocin. Purified IleRs-R2 shows no sensitivity to mupirocin even at a concentration of 5 mM, 100'000 fold higher than the Ki value of IleRS-R1. HAMAP-Rule MF_02002
Sequence similarities	Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily.

Ontologies

Keywords
Biological process	Antibiotic resistance Protein biosynthesis
Cellular component	Cytoplasm
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Aminoacyl-tRNA synthetase Ligase
Gene Ontology (GO)
Biological_process	isoleucyl-tRNA aminoacylation Inferred from electronic annotation. Source: HAMAP regulation of translational fidelity Inferred from electronic annotation. Source: GOC response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW
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 – 943	943	Isoleucine--tRNA ligase 1 HAMAP-Rule MF_02002		PRO_0000098445
Regions
	Motif	58 – 68	11	"HIGH" region HAMAP-Rule MF_02002
	Motif	608 – 612	5	"KMSKS" region HAMAP-Rule MF_02002
Sites
	Metal binding	906	1	Zinc By similarity
	Metal binding	909	1	Zinc By similarity
	Metal binding	926	1	Zinc By similarity
	Metal binding	929	1	Zinc By similarity
	Binding site	567	1	Aminoacyl-adenylate By similarity
	Binding site	611	1	ATP By similarity
Experimental info
	Sequence conflict	28 – 29	2	IL → SC Ref.2
	Sequence conflict	755 – 756	2	QT → DR Ref.2
	Sequence conflict	758 – 759	2	LY → VP Ref.2
	Sequence conflict	761 – 764	4	ISEA → QRR Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P18330 [UniParc]. Last modified November 1, 1995. Version 2. Checksum: 6827B2BF2EB89FC0	FASTA	943	105,719
	10 20 30 40 50 60 MTDYKATLNL PDTAFPMKAG LPQREPQILQ RWNSIGLYGK LREIGKDRPK FVLHDGPPYA 70 80 90 100 110 120 NGTIHIGHAL NKILKDMILR SKTLSGFDAP YVPGWDCHGL PIEHKVEVTY GKNLGADKTR 130 140 150 160 170 180 ELCRAYATEQ IEGQKSEFIR LGVLGEWDNP YKTMNFKNEA GEIRALAEIV KGGFVFKGLK 190 200 210 220 230 240 PVNWCFDCGS ALAEAEVEYE DKKSSTIDVA FPIADDAKLA EAFGLASLAK PAAIVIWTTT 250 260 270 280 290 300 PWTIPANQAL NVHPEFTYAL VDVGDRLLVL AEEMVESCLA RYELQGSVIA TATGSALELI 310 320 330 340 350 360 NFRHPFYDRL SPVYLADYVE LGSGTGIVHC SPAYGVDDFV ICKKYGMVND DIINPVQSNG 370 380 390 400 410 420 VYVPSLEFFG GQFIFKADQP IIEKLREVGA LMQTAAIQHS YMHCWRHKTP LIYRATAQWF 430 440 450 460 470 480 IGMDKEPTSG DTLRVRSLKA IEDTKFVPSW GQARLHSMIA NRPDWCISRQ RNWGVPIPFF 490 500 510 520 530 540 LNKESGELHP RTVELMEVVA QRVEQQGIEA WFKLDAAELL GDEAPLYDKI SDTLDVWFDS 550 560 570 580 590 600 GTTHWHVLRG SHPMGHETGP RADLYLEGSD QHRGWFHSSL LTGCAIDNHA PYRELLTHGF 610 620 630 640 650 660 TVDETGRKMS KSLKNVIEPK KINDTLGADI MRLWVASTDY SGEIAVSDQI LARSADAYRR 670 680 690 700 710 720 IRNTARFMLS NLTGFNPASD LLPAEDMLAL DRWAVDRTLL LQRELQEHYG EYRFWNVYSK 730 740 750 760 770 780 IHNFCVQELG GFYLDIIKDR QYTTGANSKA RRSAQTALYH ISEALVRWIA PILAFTADEL 790 800 810 820 830 840 WEYLPGERNE SVMLNTWYEG LTELPADFEL GREYWEGVMA VKVAVNKELE VQRAAKAVGG 850 860 870 880 890 900 NLQAEVTLFA EDGLTADLAK LSNELRFVLI TSTASLAPFT QAPADAVATE VPGLKLKVVK 910 920 930 940 SAFPKCARCW HCREDVGVNP EHPEICGRCV DNISGEGEVR HYA

References

[1]	"Relationship of protein structure of isoleucyl-tRNA synthetase with pseudomonic acid resistance of Escherichia coli. A proposed mode of action of pseudomonic acid as an inhibitor of isoleucyl-tRNA synthetase." Yanagisawa T., Lee J.T., Wu H.C., Kawakami M. J. Biol. Chem. 269:24304-24309(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 49323 / NCIMB 10586.
[2]	"Nucleotide sequence of the Pseudomonas fluorescens signal peptidase II gene (lsp) and flanking genes." Isaki L., Beers R., Wu H.C. J. Bacteriol. 172:6512-6517(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-29 AND 701-943. Strain: ATCC 49323 / NCIMB 10586.
[3]	"How does Pseudomonas fluorescens avoid suicide from its antibiotic pseudomonic acid? Evidence for two evolutionarily distinct isoleucyl-tRNA synthetases conferring self-defense." Yanagisawa T., Kawakami M. J. Biol. Chem. 278:25887-25894(2003) [PubMed] [Europe PMC] [Abstract] Cited for: RESISTANCE TO MUPIROCIN. Strain: ATCC 49323 / NCIMB 10586.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X80132 Genomic DNA. Translation: CAA56431.1. M35366 Genomic DNA. Translation: AAA25883.1. M35367 Genomic DNA. Translation: AAA26022.1. Sequence problems.
PIR	A37152.
3D structure databases
ProteinModelPortal	P18330.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Enzyme and pathway databases
SABIO-RK	P18330.
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

SYI1_PSEFL

Accession

Primary (citable) accession number: P18330

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1990
Last sequence update:	November 1, 1995
Last modified:	April 3, 2013
This is version 96 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program