Isoleucyl-tRNA synthetase - Escherichia coli (strain K12)

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Reviewed, UniProtKB/Swiss-Prot P00956 (SYI_ECOLI)

Last modified June 16, 2009. Version 107. History...

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

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Names and origin

Protein names

Recommended name:
    Isoleucyl-tRNA synthetase
    EC=6.1.1.5
Alternative name(s):
    Isoleucine--tRNA ligase
      Short name=IleRS

Gene names

Name:	ileS
Synonyms:	ilvS
Ordered Locus Names:	b0026, JW0024

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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Protein attributes

Sequence length	938 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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). HAMAP MF_02002
Catalytic activity	ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile). HAMAP MF_02002
Cofactor	Binds 1 zinc ion per subunit. HAMAP MF_02002
Subunit structure	Monomer. HAMAP MF_02002
Subcellular location	Cytoplasm. HAMAP 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 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. HAMAP MF_02002
Sequence similarities	Belongs to the class-I aminoacyl-tRNA synthetase family. IleS type 1 subfamily.
biophysicochemical properties	Kinetic parameters: K_M=5 µM for isoleucine Ref.9 K_M=0.4 mM for ATP

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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
PTM	Acetylation
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	isoleucyl-tRNA aminoacylation Inferred from electronic annotation. Source: HAMAP 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 isoleucine-tRNA ligase activity Inferred from electronic annotation. Source: HAMAP protein binding Inferred from physical interaction. Source: IntAct zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct	Notes
tufA	P0A6N1	1	EBI-552928,EBI-301077

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.2

Chain

2 – 938

937

Isoleucyl-tRNA synthetase HAMAP MF_02002

PRO_0000098384

Regions

Motif

58 – 68

"HIGH" region HAMAP MF_02002

Motif

602 – 606

"KMSKS" region HAMAP MF_02002

Sites

Metal binding

901

Zinc By similarity

Metal binding

904

Zinc By similarity

Metal binding

921

Zinc By similarity

Metal binding

924

Zinc By similarity

Binding site

561

Aminoacyl-adenylate By similarity

Binding site

605

ATP By similarity

Amino acid modifications

Modified residue

183

N6-acetyllysine Ref.16

Natural variations

Natural variant

594

F → L in strain: PS102. HAMAP MF_02002

Experimental info

Mutagenesis

G → R: 6000-fold increase in Km for isoleucine and 4-fold increase in Km for ATP, with no effect on activity. Ref.9

Mutagenesis

C → S: No effect on activity. Ref.9

Mutagenesis

102

I → N: No significant effect on activity. Ref.9

Mutagenesis

183

K → 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.15

Mutagenesis

241

T → A: Nearly the same editing activity as the wild-type. Ref.10

Mutagenesis

242

T → A: Abolishes editing activity against valine, with little change in aminoacylation activity; when associated with A-250. Ref.12

Mutagenesis

242

T → P: Abolishes editing activity against valine, with little change in aminoacylation activity. Ref.12

Mutagenesis

243

T → A: Abolishes editing activity against valine, with little change in aminoacylation activity. Ref.10 Ref.13

Mutagenesis

243

T → R: Abolishes pretransfer editing. Ref.10 Ref.13

Mutagenesis

246

T → A: Nearly the same editing activity as the wild-type. Ref.10

Mutagenesis

250

N → A: Abolishes editing activity against valine, with little change in aminoacylation activity. Ref.10 Ref.12

Mutagenesis

333

H → A: Alters the specificity for hydrolysis of the aminoacyl tRNA ester, with no effect on pretransfer editing. Ref.13

Mutagenesis

342

D → A or N: Strong decrease in total editing and deacylation activities. Severely deficient in translocation from the aminoacylation site to the editing site. Ref.14

Mutagenesis

342

D → 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.14

Mutagenesis

421

W → 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.15

Sequence conflict

243 – 264

TPWTL…DYALV → RRGLCLPTAQSLLHQISTMR WW AA sequence Ref.1

Sequence conflict

300 – 301

EL → DV AA sequence Ref.1

Sequence conflict

587

R → C AA sequence Ref.1

Sequence conflict

637

E → Q AA sequence Ref.1

Sequence conflict

724

G → V AA sequence Ref.1

Sequence conflict

738

A → P AA sequence Ref.1

Sequence conflict

740 – 743

ADSV → RTVW AA sequence Ref.1

Sequence conflict

787

F → L AA sequence Ref.1

Sequence conflict

830

K → N AA sequence Ref.1

Sequence conflict

867 – 869

GAT → DRRY AA sequence Ref.1

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Sequences

Sequence

Length

Mass (Da)

Tools

P00956-1 [UniParc].

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

938

104,297

        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

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References

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[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: 6390679] [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: 7929087] [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: 1630901] [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 277:1453-1474(1997) [PubMed: 9278503] [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: 16738553] [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: 2985604] [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: 6378662] [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: 6374664] [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: 3282306] [Abstract] Cited for: MUTAGENESIS OF GLY-94; CYS-97 AND ILE-102, KINETIC PARAMETERS.
[10]	"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: MUTAGENESIS OF THR-241; THR-243; THR-246 AND ASN-250.
[11]	"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: 10549284] [Abstract] Cited for: EDITING ACTIVITY.
[12]	"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: 10889024] [Abstract] Cited for: MUTAGENESIS OF THR-242 AND ASN-250.
[13]	"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: 11864608] [Abstract] Cited for: MUTAGENESIS OF THR-243 AND HIS-333, PRESENCE OF TWO EDITING SUBSITES.
[14]	"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: 11782529] [Abstract] Cited for: MUTAGENESIS OF ASP-342, TRANSLOCATION OF MISACTIVATED VALINE.
[15]	"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: 12515858] [Abstract] Cited for: MUTAGENESIS OF LYS-183 AND TRP-421.
[16]	"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: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-183, MASS SPECTROMETRY.

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Cross-references

Sequence databases
	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.
PIR	SYECIT. B64723.
RefSeq	AP_000690.1. NP_414567.1.
3D structure databases
HSSP	HSSP built from PDB template 1FFY based on UniProtKB P41972.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:10017N.
IntAct	P00956. 14 interactions.
2-D gel databases
ECO2DBASE	F107.0. 6TH EDITION.
Genome annotation databases
GeneID	944761.
GenomeReviews	Gene locus JW0024 in contig AP009048_GR. Gene locus b0026 in contig U00096_GR.
KEGG	ecj:JW0024. eco:b0026.
Organism-specific databases
EchoBASE	EB0487.
EcoGene	EG10492. ileS.
CMR	Search...
Phylogenomic databases
HOGENOM	P00956.
OMA	P00956. FPMRGNL.
Enzyme and pathway databases
BioCyc	EcoCyc:ILES-MON. MetaCyc:ILES-MON.
Family and domain databases
HAMAP	MF_02002. [Tree]
InterPro	IPR001412. aa-tRNA-synth_I_CS. IPR002300. aa-tRNA-synth_Ia. IPR010663. DNA_glyclase/IsotRNA_synth_Znf. 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]
Gene3D	G3DSA:3.40.50.620. Rossmann-like_a/b/a_fold. 1 hit.
PANTHER	PTHR11946:SF9. Ile-tRNA-synt_Ia. 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.
TIGRFAMs	TIGR00392. ileS. 1 hit.
PROSITE	PS00178. AA_TRNA_LIGASE_I. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
BindingDB	P00956.

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Entry information

Entry name

SYI_ECOLI

Accession

Primary (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:	June 16, 2009
This is version 107 of the entry and version 5 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

Aminoacyl-tRNA synthetases

List of aminoacyl-tRNA synthetase entries

Escherichia coli

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

SIMILARITY comments

Index of protein domains and families

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Natural variations

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2-D gel databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other Resources

Entry information

Relevant documents