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P00956 (SYI_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 154. 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
Synonyms:ilvS
Ordered Locus Names:b0026, JW0024
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length938 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
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). 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.

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)). HAMAP-Rule MF_02002

Miscellaneous

Strain PS102 is resistant to the antibiotic mupirocin (pseudomonic acid A), an Ile-analog that competitively inhibits activation by Ile-tRNA synthetase, thus inhibiting protein biosynthesis.

Sequence similarities

Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily.

Biophysicochemical properties

Kinetic parameters:

KM=5 µM for isoleucine Ref.9

KM=0.4 mM for ATP

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.2
Chain2 – 938937Isoleucine--tRNA ligase HAMAP-Rule MF_02002
PRO_0000098384

Regions

Motif58 – 6811"HIGH" region HAMAP-Rule MF_02002
Motif602 – 6065"KMSKS" region HAMAP-Rule MF_02002

Sites

Metal binding9011Zinc By similarity
Metal binding9041Zinc By similarity
Metal binding9211Zinc By similarity
Metal binding9241Zinc By similarity
Binding site5611Aminoacyl-adenylate By similarity
Binding site6051ATP By similarity

Amino acid modifications

Modified residue1831N6-acetyllysine Ref.17

Natural variations

Natural variant5941F → L in strain: PS102.

Experimental info

Mutagenesis941G → R: 6000-fold increase in Km for isoleucine and 4-fold increase in Km for ATP, with no effect on activity. Ref.9
Mutagenesis971C → S: No effect on activity. Ref.9
Mutagenesis1021I → N: No significant effect on activity. Ref.9
Mutagenesis1831K → A: Abolishes translocation from the aminoacylation site to the editing site, without effect on aminoacylation activity and posttransfer editing; when associated with A-421. Ref.16
Mutagenesis2411T → A: Nearly the same editing activity as the wild-type. Ref.11
Mutagenesis2421T → A: Abolishes editing activity against valine, with little change in aminoacylation activity; when associated with A-250. Ref.13
Mutagenesis2421T → P: Abolishes editing activity against valine, with little change in aminoacylation activity. Ref.13
Mutagenesis2431T → A: Abolishes editing activity against valine, with little change in aminoacylation activity. Ref.11 Ref.14
Mutagenesis2431T → R: Abolishes pretransfer editing. Ref.11 Ref.14
Mutagenesis2461T → A: Nearly the same editing activity as the wild-type. Ref.11
Mutagenesis2501N → A: Abolishes editing activity against valine, with little change in aminoacylation activity. Ref.11 Ref.13
Mutagenesis3331H → A: Alters the specificity for hydrolysis of the aminoacyl tRNA ester, with no effect on pretransfer editing. Ref.14
Mutagenesis3421D → A or N: Strong decrease in total editing and deacylation activities. Severely deficient in translocation from the aminoacylation site to the editing site. Ref.15
Mutagenesis3421D → E: Reduces 2- to 3-fold the total editing activity and 2-fold the deacylation activity. Moderately reduces translocation from the aminoacylation site to the editing site. Ref.15
Mutagenesis4211W → A: Abolishes translocation from the aminoacylation site to the editing site, without effect on aminoacylation activity and posttransfer editing; when associated with A-183. Ref.16
Sequence conflict243 – 26422TPWTL…DYALV → RRGLCLPTAQSLLHQISTMR WW AA sequence Ref.1
Sequence conflict300 – 3012EL → DV AA sequence Ref.1
Sequence conflict5871R → C AA sequence Ref.1
Sequence conflict6371E → Q AA sequence Ref.1
Sequence conflict7241G → V AA sequence Ref.1
Sequence conflict7381A → P AA sequence Ref.1
Sequence conflict740 – 7434ADSV → RTVW AA sequence Ref.1
Sequence conflict7871F → L AA sequence Ref.1
Sequence conflict8301K → N AA sequence Ref.1
Sequence conflict867 – 8693GAT → DRRY AA sequence Ref.1

Sequences

Sequence LengthMass (Da)Tools
P00956 [UniParc].

Last modified January 23, 2007. Version 5.
Checksum: 238CEDAF461F01D5

FASTA938104,297
        10         20         30         40         50         60 
MSDYKSTLNL PETGFPMRGD LAKREPGMLA RWTDDDLYGI IRAAKKGKKT FILHDGPPYA 

        70         80         90        100        110        120 
NGSIHIGHSV NKILKDIIVK SKGLSGYDSP YVPGWDCHGL PIELKVEQEY GKPGEKFTAA 

       130        140        150        160        170        180 
EFRAKCREYA ATQVDGQRKD FIRLGVLGDW SHPYLTMDFK TEANIIRALG KIIGNGHLHK 

       190        200        210        220        230        240 
GAKPVHWCVD CRSALAEAEV EYYDKTSPSI DVAFQAVDQD ALKAKFAVSN VNGPISLVIW 

       250        260        270        280        290        300 
TTTPWTLPAN RAISIAPDFD YALVQIDGQA VILAKDLVES VMQRIGVTDY TILGTVKGAE 

       310        320        330        340        350        360 
LELLRFTHPF MGFDVPAILG DHVTLDAGTG AVHTAPGHGP DDYVIGQKYG LETANPVGPD 

       370        380        390        400        410        420 
GTYLPGTYPT LDGVNVFKAN DIVVALLQEK GALLHVEKMQ HSYPCCWRHK TPIIFRATPQ 

       430        440        450        460        470        480 
WFVSMDQKGL RAQSLKEIKG VQWIPDWGQA RIESMVANRP DWCISRQRTW GVPMSLFVHK 

       490        500        510        520        530        540 
DTEELHPRTL ELMEEVAKRV EVDGIQAWWD LDAKEILGDE ADQYVKVPDT LDVWFDSGST 

       550        560        570        580        590        600 
HSSVVDVRPE FAGHAADMYL EGSDQHRGWF MSSLMISTAM KGKAPYRQVL THGFTVDGQG 

       610        620        630        640        650        660 
RKMSKSIGNT VSPQDVMNKL GADILRLWVA STDYTGEMAV SDEILKRAAD SYRRIRNTAR 

       670        680        690        700        710        720 
FLLANLNGFD PAKDMVKPEE MVVLDRWAVG CAKAAQEDIL KAYEAYDFHE VVQRLMRFCS 

       730        740        750        760        770        780 
VEMGSFYLDI IKDRQYTAKA DSVARRSCQT ALYHIAEALV RWMAPILSFT ADEVWGYLPG 

       790        800        810        820        830        840 
EREKYVFTGE WYEGLFGLAD SEAMNDAFWD ELLKVRGEVN KVIEQARADK KVGGSLEAAV 

       850        860        870        880        890        900 
TLYAEPELSA KLTALGDELR FVLLTSGATV ADYNDAPADA QQSEVLKGLK VALSKAEGEK 

       910        920        930 
CPRCWHYTQD VGKVAEHAEI CGRCVSNVAG DGEKRKFA 

« Hide

References

« Hide 'large scale' references
[1]"Specific sequence homology and three-dimensional structure of an aminoacyl transfer RNA synthetase."
Webster T., Tsai H., Kula M., Mackie G.A., Schimmel P.
Science 226:1315-1317(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
[2]"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], PROTEIN SEQUENCE OF 2-11 AND 606-615.
Strain: K12 / MC4100 / ATCC 35695 / DSM 6574 and PS102.
[3]"Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region."
Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A.
Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12.
[4]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[5]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION.
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]"Characterization of the ileS-lsp operon in Escherichia coli. Identification of an open reading frame upstream of the ileS gene and potential promoter(s) for the ileS-lsp operon."
Kamio Y., Lin C.-K., Regue M., Wu H.C.
J. Biol. Chem. 260:5616-5620(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-71.
[7]"Nucleotide sequence of the lspA gene, the structural gene for lipoprotein signal peptidase of Escherichia coli."
Yu F., Yamada H., Daishima K., Mizushima S.
FEBS Lett. 173:264-268(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 794-938.
[8]"Nucleotide sequence of the Escherichia coli prolipoprotein signal peptidase (lsp) gene."
Innis M.A., Tokunaga M., Williams M.E., Loranger J.M., Chang S.-Y., Chang S., Wu H.C.
Proc. Natl. Acad. Sci. U.S.A. 81:3708-3712(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 795-938.
[9]"Evidence from cassette mutagenesis for a structure-function motif in a protein of unknown structure."
Clarke N.D., Lien D.C., Schimmel P.
Science 240:521-523(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLY-94; CYS-97 AND ILE-102, KINETIC PARAMETERS.
[10]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[11]"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: MUTAGENESIS OF THR-241; THR-243; THR-246 AND ASN-250.
[12]"Transfer RNA-dependent translocation of misactivated amino acids to prevent errors in protein synthesis."
Nomanbhoy T.K., Hendrickson T.L., Schimmel P.
Mol. Cell 4:519-528(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: EDITING ACTIVITY.
[13]"Errors from selective disruption of the editing center in a tRNA synthetase."
Hendrickson T.L., Nomanbhoy T.K., Schimmel P.
Biochemistry 39:8180-8186(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF THR-242 AND ASN-250.
[14]"Mutational separation of two pathways for editing by a class I tRNA synthetase."
Hendrickson T.L., Nomanbhoy T.K., de Crecy-Lagard V., Fukai S., Nureki O., Yokoyama S., Schimmel P.
Mol. Cell 9:353-362(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF THR-243 AND HIS-333, PRESENCE OF TWO EDITING SUBSITES.
[15]"Blocking site-to-site translocation of a misactivatd amino acid by mutation of a class I tRNA synthetase."
Bishop A.C., Nomanbhoy T.K., Schimmel P.
Proc. Natl. Acad. Sci. U.S.A. 99:585-590(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF ASP-342, TRANSLOCATION OF MISACTIVATED VALINE.
[16]"Interstice mutations that block site-to-site translocation of a misactivated amino acid bound to a class I tRNA synthetase."
Bishop A.C., Beebe K., Schimmel P.R.
Proc. Natl. Acad. Sci. U.S.A. 100:490-494(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF LYS-183 AND TRP-421.
[17]"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-183, IDENTIFICATION BY MASS SPECTROMETRY.
Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U00096 Genomic DNA. Translation: AAC73137.1.
AP009048 Genomic DNA. Translation: BAB96595.2.
M10428 Genomic DNA. Translation: AAA24606.1.
X00776 Genomic DNA. Translation: CAA25352.1.
K01990 Genomic DNA. Translation: AAA24091.1.
PIRSYECIT. B64723.
RefSeqNP_414567.1. NC_000913.3.
YP_488332.1. NC_007779.1.

3D structure databases

ProteinModelPortalP00956.
SMRP00956. Positions 3-882.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid849163. 1 interaction.
DIPDIP-10017N.
IntActP00956. 16 interactions.
MINTMINT-1232480.
STRING511145.b0026.

Chemistry

BindingDBP00956.
ChEMBLCHEMBL3657.

Proteomic databases

PaxDbP00956.
PRIDEP00956.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC73137; AAC73137; b0026.
BAB96595; BAB96595; BAB96595.
GeneID12932381.
944761.
KEGGecj:Y75_p0026.
eco:b0026.
PATRIC32115143. VBIEscCol129921_0023.

Organism-specific databases

EchoBASEEB0487.
EcoGeneEG10492. ileS.

Phylogenomic databases

eggNOGCOG0060.
HOGENOMHOG000246402.
KOK01870.
OMAKPVHWCL.
OrthoDBEOG644ZM1.
PhylomeDBP00956.

Enzyme and pathway databases

BioCycEcoCyc:ILES-MONOMER.
ECOL316407:JW0024-MONOMER.
MetaCyc:ILES-MONOMER.

Gene expression databases

GenevestigatorP00956.

Family and domain databases

Gene3D1.10.730.10. 1 hit.
3.40.50.620. 2 hits.
3.90.740.10. 1 hit.
HAMAPMF_02002. Ile_tRNA_synth_type1.
InterProIPR001412. 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]
PANTHERPTHR11946:SF9. PTHR11946:SF9. 1 hit.
PfamPF08264. Anticodon_1. 1 hit.
PF00133. tRNA-synt_1. 1 hit.
PF06827. zf-FPG_IleRS. 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

PROP00956.

Entry information

Entry nameSYI_ECOLI
AccessionPrimary (citable) accession number: P00956
Secondary accession number(s): P78038, Q59429
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: May 14, 2014
This is version 154 of the entry and version 5 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

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries