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P56690 (SYI_THET8) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 101. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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:TTHA1067
OrganismThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Reference proteome] [HAMAP]
Taxonomic identifier300852 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Protein attributes

Sequence length1043 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

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_02003

Catalytic activity

ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile). HAMAP-Rule MF_02003

Cofactor

Binds 2 zinc ions per subunit.

Subunit structure

Monomer.

Subcellular location

Cytoplasm HAMAP-Rule MF_02003.

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_02003

Miscellaneous

The ATP consumption with regard to L-valine is nonproductive and is solely for substrate selection, which demonstrates the high cost of accuracy.

Sequence similarities

Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 2 subfamily.

Ontologies

Keywords
   Biological processProtein biosynthesis
   Cellular componentCytoplasm
   LigandATP-binding
Metal-binding
Nucleotide-binding
Zinc
   Molecular functionAminoacyl-tRNA synthetase
Ligase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processisoleucyl-tRNA aminoacylation

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

aminoacyl-tRNA editing activity

Inferred from electronic annotation. Source: InterPro

isoleucine-tRNA ligase activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

zinc ion binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 10431043Isoleucine--tRNA ligase HAMAP-Rule MF_02003
PRO_0000098567

Regions

Motif47 – 5711"HIGH" region HAMAP-Rule MF_02003
Motif591 – 5955"KMSKS" region HAMAP-Rule MF_02003

Sites

Metal binding1811Zinc 1
Metal binding1841Zinc 1
Metal binding3891Zinc 1
Metal binding3921Zinc 1
Metal binding4611Zinc 2
Metal binding4641Zinc 2
Metal binding5021Zinc 2
Metal binding5041Zinc 2
Binding site571Aminoacyl-adenylate
Binding site3191Valine
Binding site3281Valine
Binding site5501Aminoacyl-adenylate
Binding site5531Aminoacyl-adenylate
Binding site5541Aminoacyl-adenylate
Binding site5811Aminoacyl-adenylate
Binding site5941ATP By similarity

Experimental info

Mutagenesis2281T → A: Has some defects in posttransfer editing activity. Ref.4
Mutagenesis2291T → A: Has some defects in posttransfer editing activity. Ref.4
Mutagenesis2301T → A: No change in posttransfer editing activity. Ref.4
Mutagenesis2331T → A: No change in posttransfer editing activity. Ref.4
Mutagenesis3281D → A: Has some defects in posttransfer editing activity. Ref.4

Secondary structure

................................................................................................................................................. 1043
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P56690 [UniParc].

Last modified March 29, 2005. Version 2.
Checksum: 0F8010BBE8F83A30

FASTA1,043119,247
        10         20         30         40         50         60 
MFKEVGEPNF PKLEEEVLAF WKREKIFQKS VENRKGGPRY TVYEGPPTAN GLPHVGHAQA 

        70         80         90        100        110        120 
RSYKDLFPRY KTMRGYYAPR RAGWDTHGLP VELEVEKKLG LKSKREIEAY GIERFNQACR 

       130        140        150        160        170        180 
ESVFTYEKEW EAFTERIAYW VDLENAYATL EPTYIESIWW SLKNLFDRGL LYRDHKVVPY 

       190        200        210        220        230        240 
CPRCGTPLSS HEVALGYKEI QDPSVYVRFP LKEPKKLGLE KASLLIWTTT PWTLPGNVAA 

       250        260        270        280        290        300 
AVHPEYTYAA FQVGDEALIL EEGLGRKLLG EGTPVLKTFP GKALEGLPYT PPYPQALEKG 

       310        320        330        340        350        360 
YFVVLADYVS QEDGTGIVHQ APAFGAEDLE TARVYGLPLL KTVDEEGKLL VEPFKGLYFR 

       370        380        390        400        410        420 
EANRAILRDL RGRGLLFKEE SYLHSYPHCW RCSTPLMYYA TESWFIKNTL FKDELIRKNQ 

       430        440        450        460        470        480 
EIHWVPPHIK EGRYGEWLKN LVDWALSRNR YWGTPLPIWV CQACGKEEAI GSFQELKARA 

       490        500        510        520        530        540 
TKPLPEPFDP HRPYVDQVEL ACACGGTMRR VPYVIDVWYD SGAMPFASLH YPFEHEEVFR 

       550        560        570        580        590        600 
ESFPADFIAE GIDQTRGWFN SLHQLGVMLF GSIAFKNVIC HGLILDEKGQ KMSKSKGNVV 

       610        620        630        640        650        660 
DPWDIIREFG ADALRWYIYV SAPPEADRRF GPNLVRETVR DYFLTLWNVY SFFVTYANLD 

       670        680        690        700        710        720 
RPDLKNPPPP EKRPEMDRWL LARMQDLIQR VTEALEAYDP TTSARALRDF VVEDLSQWYV 

       730        740        750        760        770        780 
RRNRRRFWKN EDALDREAAY ATLYEALVLV ATLAAPFTPF LAEVLWQNLV RSVRPEAKES 

       790        800        810        820        830        840 
VHLADWPEAD PALADEALVA QMRAVLKVVD LARAARAKSG VKTRTPLPLL LVTAPTALER 

       850        860        870        880        890        900 
EGLKRFAHEI AEELNVKEVR VLEPGEEILS YRVLPNLKLL GRKYGKLVPK IREALQRERE 

       910        920        930        940        950        960 
RAAALALKGE AIPLEVEGEA LTLLPEEVLL EAEAPKGYQA LEKDGYVAAL KVEVTEALRM 

       970        980        990       1000       1010       1020 
EGLARDLIRL LQQARKDMGL KVSDRIRVGY EAEGPYLEAL KRHGPWIAEE VLATAFGEGL 

      1030       1040 
FGGFEARVED EEGKAVFHLA RAE 

« Hide

References

« Hide 'large scale' references
[1]"Complete genome sequence of Thermus thermophilus HB8."
Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: HB8 / ATCC 27634 / DSM 579.
[2]"Enzyme structure with two catalytic sites for double-sieve selection of substrate."
Nureki O., Vassylyev D.G., Tateno M., Shimada A., Nakama T., Fukai S., Konno M., Hendrickson T.L., Schimmel P., Yokoyama S.
Science 280:578-582(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-821 IN COMPLEX WITH ZINC IONS.
[3]"Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase."
Nakama T., Nureki O., Yokoyama S.
J. Biol. Chem. 276:47387-47393(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-821 IN COMPLEX WITH ZINC IONS; ILE-ADENYLATE AND MUPIROCIN.
[4]"Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine."
Fukunaga R., Fukai S., Ishitani R., Nureki O., Yokoyama S.
J. Biol. Chem. 279:8396-8402(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH VAL, MUTAGENESIS OF THR-228; THR-229; THR-230; THR-233 AND ASP-328.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AP008226 Genomic DNA. Translation: BAD70890.1.
RefSeqYP_144333.1. NC_006461.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ILEX-ray2.50A1-821[»]
1JZQX-ray3.00A1-821[»]
1JZSX-ray2.50A1-821[»]
1UDZX-ray1.80A/B201-381[»]
1UE0X-ray2.00A/B201-381[»]
1WK8X-ray1.70A/B196-388[»]
1WNYX-ray1.60A/B201-385[»]
1WNZX-ray1.70A201-385[»]
ProteinModelPortalP56690.
SMRP56690. Positions 1-821.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING300852.TTHA1067.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAD70890; BAD70890; BAD70890.
GeneID3168241.
KEGGttj:TTHA1067.
PATRIC23957094. VBITheThe93045_1047.

Phylogenomic databases

eggNOGCOG0060.
HOGENOMHOG000246403.
KOK01870.
OMARVEHMVE.
OrthoDBEOG644ZM1.
PhylomeDBP56690.

Enzyme and pathway databases

BioCycTTHE300852:GH8R-1099-MONOMER.

Family and domain databases

Gene3D1.10.730.10. 1 hit.
3.40.50.620. 2 hits.
3.90.740.10. 1 hit.
HAMAPMF_02003. Ile_tRNA_synth_type2.
InterProIPR001412. aa-tRNA-synth_I_CS.
IPR002300. aa-tRNA-synth_Ia.
IPR002301. Ile-tRNA-ligase.
IPR023586. Ile-tRNA-ligase_type2.
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.
[Graphical view]
PfamPF08264. Anticodon_1. 1 hit.
PF00133. tRNA-synt_1. 1 hit.
[Graphical view]
PRINTSPR00984. TRNASYNTHILE.
SUPFAMSSF47323. SSF47323. 1 hit.
SSF50677. SSF50677. 1 hit.
TIGRFAMsTIGR00392. ileS. 1 hit.
PROSITEPS00178. AA_TRNA_LIGASE_I. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP56690.

Entry information

Entry nameSYI_THET8
AccessionPrimary (citable) accession number: P56690
Secondary accession number(s): Q5SJE7
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: March 29, 2005
Last modified: July 9, 2014
This is version 101 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries