EzCatDB: M00177
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DB codeM00177
CATH domainDomain 13.40.50.620 : Rossmann foldCatalytic domain
Domain 23.90.740.10 : Isoleucyl-tRNA Synthetase; domain 2
Domain 31.10.730.10 : Isoleucyl-tRNA Synthetase; Domain 1
Domain 42.-.-.-
E.C.6.1.1.5
MACiEM0309

CATH domainRelated DB codes (homologues)
1.10.730.10 : Isoleucyl-tRNA Synthetase; Domain 1T00106
3.40.50.620 : Rossmann foldS00314,S00549,S00316,S00317,S00318,S00315,T00085,T00249,D00300,M00178,T00106,T00114

Enzyme Name
UniProtKBKEGG

P41972P56690
Protein nameIsoleucyl-tRNA synthetaseIsoleucyl-tRNA synthetaseisoleucine---tRNA ligase
isoleucyl-tRNA synthetase
isoleucyl-transfer ribonucleate synthetase
isoleucyl-transfer RNA synthetase
isoleucine-transfer RNA ligase
isoleucine-tRNA synthetase
isoleucine translase
SynonymsEC 6.1.1.5
Isoleucine--tRNA ligase
IleRS
EC 6.1.1.5
Isoleucine--tRNA ligase
IleRS
RefSeq
YP_144333.1 (Protein)
NC_006461.1 (DNA/RNA sequence)
PfamPF08264 (Anticodon_1)
PF00133 (tRNA-synt_1)
PF06827 (zf-FPG_IleRS)
[Graphical view]
PF08264 (Anticodon_1)
PF00133 (tRNA-synt_1)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00290Valine, leucine and isoleucine biosynthesis
MAP00970Aminoacyl-tRNA biosynthesis

UniProtKB:Accession NumberP41972P56690
Entry nameSYI1_STAAUSYI_THET8
ActivityATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile).ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl-tRNA(Ile).
SubunitMonomer.Monomer.
Subcellular locationCytoplasm.Cytoplasm.
CofactorBinds 1 zinc ion per subunit.Binds 2 zinc ions per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00038C00002C00407C01644C00020C00013C03127
CompoundZincATPL-IsoleucinetRNA(Ile)AMPPyrophosphateL-Isoleucyl-tRNA(Ile)Isoleucinyl-adenylate
Typeheavy metalamine group,nucleotideamino acidsnucleic acidsamine group,nucleotidephosphate group/phosphate ionamino acids,nucleic acids
ChEBI29105
15422
17191
58045

16027
29888


PubChem32051
5957
7043901
6306

6083
21961011
1023


                
1ffyA01UnboundUnboundUnboundAnalogue:C-C-C-A-C(chain T:3'-terminus)UnboundUnboundUnboundUnbound
1qu2A01UnboundUnboundUnboundAnalogue:C-C-C-A-C(chain T:3'-terminus)UnboundUnboundUnboundUnbound
1qu3A01UnboundUnboundUnboundAnalogue:C-C-C-A-C(chain T:3'-terminus)UnboundUnboundUnboundUnbound
1ileA03Bound:2x_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1jzqA03Bound:2x_ZNUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:ILA
1jzsA03Bound:2x_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ffyA02Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1qu2A02Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1qu3A02Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ileA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1jzqA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1jzsA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1udzAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1udzBUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ue0AUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ue0BUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ffyA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1qu2A03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1qu3A03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ileA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1jzqA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1jzsA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1ffyA04Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1qu2A04Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1qu3A04UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
PDB;1jzq & literature [22]
pdbCatalytic residuesMain-chain involved in catalysis
          
1ffyA01HIS 67;LYS 595
GLY 593
1qu2A01HIS 67;LYS 595
GLY 593
1qu3A01HIS 67;LYS 595
GLY 593
1ileA03HIS 57;LYS 591
GLY 589
1jzqA03HIS 57;LYS 591
GLY 589
1jzsA03HIS 57;LYS 591
GLY 589
1ffyA02 
 
1qu2A02 
 
1qu3A02 
 
1ileA02 
 
1jzqA02 
 
1jzsA02 
 
1udzA 
 
1udzB 
 
1ue0A 
 
1ue0B 
 
1ffyA03 
 
1qu2A03 
 
1qu3A03 
 
1ileA01 
 
1jzqA01 
 
1jzsA01 
 
1ffyA04 
 
1qu2A04 
 
1qu3A04 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[22]

[28]


references
[1]
PubMed ID782885
JournalEur J Biochem
Year1976
Volume66
Pages493-7
AuthorsFreist W, von der Haar F, Faulhammer H, Cramer F
TitleValyl-tRNA, isoleucyl-tRNA and tyrosyl-tRNA synthetase from baker's yeast. Substrate specificity with regard to ATP analogs and mechanism of the aminoacylation reaction.
[2]
PubMed ID6340735
JournalBiochemistry
Year1983
Volume22
Pages1229-36
AuthorsLowe G, Sproat BS, Tansley G, Cullis PM
TitleA stereochemical and positional isotope exchange study of the mechanism of activation of isoleucine by isoleucyl-tRNA synthetase from Escherichia coli.
[3]
PubMed ID3322383
JournalBiochemistry
Year1987
Volume26
Pages6531-8
AuthorsKohda D, Kawai G, Yokoyama S, Kawakami M, Mizushima S, Miyazawa T
TitleNMR analyses of the conformations of L-isoleucine and L-valine bound to Escherichia coli isoleucyl-tRNA synthetase.
[4]
PubMed ID3282306
JournalScience
Year1988
Volume240
Pages521-3
AuthorsClarke ND, Lien DC, Schimmel P
TitleEvidence from cassette mutagenesis for a structure-function motif in a protein of unknown structure.
[5]
PubMed ID2182633
JournalJ Biol Chem
Year1990
Volume265
Pages6931-5
AuthorsKohno T, Kohda D, Haruki M, Yokoyama S, Miyazawa T
TitleNonprotein amino acid furanomycin, unlike isoleucine in chemical structure, is charged to isoleucine tRNA by isoleucyl-tRNA synthetase and incorporated into protein.
[6]
PubMed ID2183216
JournalProteins
Year1990
Volume7
Pages99-111
AuthorsBurbaum JJ, Starzyk RM, Schimmel P
TitleUnderstanding structural relationships in proteins of unsolved three-dimensional structure.
[7]
PubMed ID2025282
JournalBiochem Biophys Res Commun
Year1991
Volume176
Pages682-9
AuthorsWilliams JS, Rosevear PR
TitleNuclear overhauser effect studies of the conformations of Mg(alpha, beta-methylene)ATP bound to E. coli isoleucyl-tRNA synthetase.
[8]
PubMed ID1371507
JournalJ Biol Chem
Year1992
Volume267
Pages4592-9
AuthorsCsank C, Martindale DW
TitleIsoleucyl-tRNA synthetase from the ciliated protozoan Tetrahymena thermophila. DNA sequence, gene regulation, and leucine zipper motifs.
[9]
PubMed ID8199246
JournalBiochimie
Year1993
Volume75
Pages1109-15
AuthorsNiimi T, Kawai G, Takayanagi M, Noguchi T, Hayashi N, Kohno T, Muto Y, Watanabe K, Miyazawa T, Yokoyama S
TitleA 15N-1H nuclear magnetic resonance study on the interaction between isoleucine tRNA and isoleucyl-tRNA synthetase from Escherichia coli.
[10]
PubMed ID7947832
JournalBiochemistry
Year1994
Volume33
Pages14213-20
AuthorsLandro JA, Schmidt E, Schimmel P, Tierney DL, Penner-Hahn JE
TitleThiol ligation of two zinc atoms to a class I tRNA synthetase: evidence for unshared thiols and role in amino acid binding and utilization.
[11]
PubMed ID8286369
JournalBiochemistry
Year1994
Volume33
Pages398-402
AuthorsXu B, Trawick B, Krudy GA, Phillips RM, Zhou L, Rosevear PR
TitleProbing the metal binding sites of Escherichia coli isoleucyl-tRNA synthetase.
[12]
PubMed ID7669778
JournalBiochemistry
Year1995
Volume34
Pages11204-10
AuthorsSchmidt E, Schimmel P
TitleResidues in a class I tRNA synthetase which determine selectivity of amino acid recognition in the context of tRNA.
[13]
PubMed ID8672449
JournalBiochemistry
Year1996
Volume35
Pages4139-45
AuthorsGlasfeld E, Landro JA, Schimmel P
TitleC-terminal zinc-containing peptide required for RNA recognition by a class I tRNA synthetase.
[14]
PubMed ID8611551
JournalBiochemistry
Year1996
Volume35
Pages5596-601
AuthorsLin L, Schimmel P
TitleMutational analysis suggests the same design for editing activities of two tRNA synthetases.
[15]
PubMed ID8900273
JournalNature
Year1996
Volume384
Pages33-4
AuthorsLin L, Hale SP, Schimmel P
TitleAminoacylation error correction.
[16]
PubMed ID8692688
JournalNucleic Acids Res
Year1996
Volume24
Pages2505-10
AuthorsJakubowski H
TitleProofreading in trans by an aminoacyl-tRNA synthetase: a model for single site editing by isoleucyl-tRNA synthetase.
[17]
PubMed ID9184155
JournalBiochemistry
Year1997
Volume36
Pages6739-44
AuthorsGlasfeld E, Schimmel P
TitleZinc-dependent tRNA binding by a peptide element within a tRNA synthetase.
[18]
PubMed ID9822629
JournalJ Biol Chem
Year1998
Volume273
Pages31680-90
AuthorsPope AJ, Lapointe J, Mensah L, Benson N, Brown MJ, Moore KJ
TitleCharacterization of isoleucyl-tRNA synthetase from Staphylococcus aureus. I: Kinetic mechanism of the substrate activation reaction studied by transient and steady-state techniques.
[19]
PubMed ID9575099
JournalScience
Year1998
Volume280
Pages541
AuthorsFersht AR
TitleSieves in sequence.
[20]
PubMed ID9554847
JournalScience
Year1998
Volume280
Pages578-82
AuthorsNureki O, Vassylyev DG, Tateno M, Shimada A, Nakama T, Fukai S, Konno M, Hendrickson TL, Schimmel P, Yokoyama S
TitleEnzyme structure with two catalytic sites for double-sieve selection of substrate.
Related PDB1ile
[21]
PubMed ID10446363
JournalBiochim Biophys Acta
Year1999
Volume1433
Pages103-9
AuthorsMichaels JE, Shiba K, Miller WT
TitleAutonomous folding of a C-terminal inhibitory fragment of Escherichia coli isoleucine-tRNA synthetase.
[22]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID99377249
PubMed ID10446055
JournalScience
Year1999
Volume285
Pages1074-7
AuthorsSilvian LF, Wang J, Steitz TA
TitleInsights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin.
Related PDB1ffy,1qu2,1qu3
Related UniProtKBP41972
[23]
PubMed ID10821672
JournalBiochemistry
Year2000
Volume39
Pages6003-11
AuthorsBrown MJ, Mensah LM, Doyle ML, Broom NJ, Osbourne N, Forrest AK, Richardson CM, O'Hanlon PJ, Pope AJ
TitleRational design of femtomolar inhibitors of isoleucyl tRNA synthetase from a binding model for pseudomonic acid-A.
[24]
PubMed ID10889024
JournalBiochemistry
Year2000
Volume39
Pages8180-6
AuthorsHendrickson TL, Nomanbhoy TK, Schimmel P
TitleErrors from selective disruption of the editing center in a tRNA synthetase.
[25]
PubMed ID11732604
JournalActa Biochim Pol
Year2001
Volume48
Pages323-35
AuthorsSankaranarayanan R, Moras D
TitleThe fidelity of the translation of the genetic code.
[26]
PubMed ID11284704
JournalBiochemistry
Year2001
Volume40
Pages4478-83
AuthorsFarrow MA, Schimmel P
TitleEditing by a tRNA synthetase: DNA aptamer-induced translocation and hydrolysis of a misactivated amino acid.
[27]
PubMed ID11412966
JournalBioorg Med Chem Lett
Year2001
Volume11
Pages1485-91
AuthorsNomanbhoy TK, Schimmel P
TitleActive site of an aminoacyl-tRNA synthetase dissected by energy-transfer-dependent fluorescence.
[28]
PubMed ID11584022
JournalJ Biol Chem
Year2001
Volume276
Pages47387-93
AuthorsNakama T, Nureki O, Yokoyama S
TitleStructural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase.
Related PDB1jzq,1jzs
[29]
PubMed ID11864608
JournalMol Cell
Year2002
Volume9
Pages353-62
AuthorsHendrickson TL, Nomanbhoy TK, de Crecy-Lagard V, Fukai S, Nureki O, Yokoyama S, Schimmel P
TitleMutational separation of two pathways for editing by a class I tRNA synthetase.
[30]
PubMed ID11782529
JournalProc Natl Acad Sci U S A
Year2002
Volume99
Pages585-90
AuthorsBishop AC, Nomanbhoy TK, Schimmel P
TitleBlocking site-to-site translocation of a misactivated amino acid by mutation of a class I tRNA synthetase.
[31]
PubMed ID12515858
JournalProc Natl Acad Sci U S A
Year2003
Volume100
Pages490-4
AuthorsBishop AC, Beebe K, Schimmel PR
TitleInterstice mutations that block site-to-site translocation of a misactivated amino acid bound to a class I tRNA synthetase.
[32]
PubMed ID14672940
JournalJ Biol Chem
Year2004
Volume279
Pages8396-402
AuthorsFukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S
TitleCrystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine.
Related PDB1udz,1ue0

comments
Although this enzyme binds zinc ions, the binding sites are not conserved, away from active sites, suggesting that zinc ions are not involved in catalysis.
The detailed catalytic mechanism has not been elucidated yet. However, this enzyme catalyzes two successive transfer reactions.
(A) Transfer of the adenylate from ATP (the first substrate) to the carboxylate of the second substrate, isoleucine: This reaction results in the formation of leucinyl-adenylate (intermediate) and the release of the inorganic pyrophosphate.
(B) Transfer of the acyl group from the intermediate to the 3'-end of tRNA(Ile).

createdupdated
2004-09-142009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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