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Reviewed, UniProtKB/Swiss-Prot P56690 (SYI_THET8)

Last modified June 16, 2009. Version 62. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein namesRecommended name:
    Isoleucyl-tRNA synthetase
    EC=6.1.1.5
Alternative name(s):
    Isoleucine--tRNA ligase
      Short name=IleRS
Gene names
Name: ileS
Ordered Locus Names: TTHA1067
OrganismThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Complete proteome] [HAMAP]
Taxonomic identifier300852 [NCBI]
Taxonomic lineageBacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

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Protein attributes

Sequence length1043 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is not processed.
Protein existenceEvidence at protein level.

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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.

Catalytic activity

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

Cofactor

Binds 2 zinc ions per subunit. HAMAP MF_02003

Subunit structure

Monomer. HAMAP MF_02003

Subcellular location

Cytoplasm. HAMAP 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.

Miscellaneous

The ATP consumption with regard to L-valine is nonproductive and is solely for substrate selection, which demonstrates the high cost of accuracy. HAMAP MF_02003

Sequence similarities

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

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Ontologies

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

Inferred from electronic annotation. Source: HAMAP

   Cellular componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular functionATP binding

Inferred from electronic annotation. Source: HAMAP

isoleucine-tRNA ligase activity

Inferred from electronic annotation. Source: HAMAP

zinc ion binding

Inferred from electronic annotation. Source: HAMAP

Complete GO annotation...

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Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 10431043Isoleucyl-tRNA synthetase HAMAP MF_02003
PRO_0000098567

Regions

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

Sites

Metal binding1811Zinc 1 HAMAP MF_02003
Metal binding1841Zinc 1 HAMAP MF_02003
Metal binding3891Zinc 1 HAMAP MF_02003
Metal binding3921Zinc 1 HAMAP MF_02003
Metal binding4611Zinc 2 HAMAP MF_02003
Metal binding4641Zinc 2 HAMAP MF_02003
Metal binding5021Zinc 2 HAMAP MF_02003
Metal binding5041Zinc 2 HAMAP MF_02003
Binding site571Aminoacyl-adenylate HAMAP MF_02003
Binding site3191Valine HAMAP MF_02003
Binding site3281Valine HAMAP MF_02003
Binding site5501Aminoacyl-adenylate HAMAP MF_02003
Binding site5531Aminoacyl-adenylate HAMAP MF_02003
Binding site5541Aminoacyl-adenylate HAMAP MF_02003
Binding site5811Aminoacyl-adenylate HAMAP MF_02003
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

1 .......................................................................................................................................... 1043
Helix Strand Turn

Details...

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Sequences

Sequence LengthMass (Da)Tools
P56690-1 [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

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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].
[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: 9554847] [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: 11584022] [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: 14672940] [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.

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Cross-references

Sequence databases

AP008226 Genomic DNA. Translation: BAD70890.1.
RefSeqYP_144333.1.

3D structure databases

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[»]
ModBaseSearch...

Genome annotation databases

GeneID3168241.
GenomeReviewsGene locus TTHA1067 in contig AP008226_GR.
KEGGttj:TTHA1067.
NMPDRfig|300852.3.peg.1204.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMP56690.
OMAP56690. SNWYVRR.

Enzyme and pathway databases

BioCycTTHE300852:TTHA1067-MON.

Family and domain databases

HAMAPMF_02003.
[Tree]
InterProIPR001412. aa-tRNA-synth_I_CS.
IPR002300. aa-tRNA-synth_Ia.
IPR002301. Ile-tRNA-synt_Ia.
IPR015905. Ile-tRNA-synt_Ia_N.
IPR018353. Isoleucyl-tRNA_synthetase.
IPR014729. Rossmann-like_a/b/a_fold.
IPR013155. V/L/I-tRNA-synth_anticodon-bd.
[Graphical view]
Gene3DG3DSA:3.40.50.620. Rossmann-like_a/b/a_fold. 1 hit.
PANTHERPTHR11946:SF9. Ile-tRNA-synt_Ia. 1 hit.
PfamPF08264. Anticodon_1. 1 hit.
PF00133. tRNA-synt_1. 1 hit.
[Graphical view]
PRINTSPR00984. TRNASYNTHILE.
TIGRFAMsTIGR00392. ileS. 1 hit.
PROSITEPS00178. AA_TRNA_LIGASE_I. 1 hit.
[Graphical view]
ProtoNetSearch...

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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: June 16, 2009
This is version 62 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents