EzCatDB: M00049

DB codeM00049
RLCP classification3.113.90000.394
CATH domainDomain 13.10.20.30
Domain 23.30.980.10
Domain 33.30.54.20
Domain 43.30.930.10Catalytic domain
Domain 53.40.50.800
E.C.6.1.1.3
CSA1qf6

CATH domainRelated DB codes (homologues)
3.10.20.30M00039,M00042
3.30.930.10S00413,D00291,D00293,D00294,D00295,T00113
3.40.50.800D00295

Enzyme Name
Swiss-protKEGG

P0A8M3Q8NW68
Protein nameThreonyl-tRNA synthetaseThreonyl-tRNA synthetasethreonine---tRNA ligase
threonyl-tRNA synthetase
threonyl-transfer ribonucleate synthetase
threonyl-transfer RNA synthetase
threonyl-transfer ribonucleic acid synthetase
threonyl ribonucleic synthetase
threonine-transfer ribonucleate synthetase
threonine translase
threonyl-tRNA synthetase
TRS
SynonymsEC 6.1.1.3
Threonine--tRNA ligase
ThrRS
EC 6.1.1.3
Threonine--tRNA ligase
ThrRS

KEGG pathways
MAP codePathways
MAP00260Glycine, serine and threonine metabolism
MAP00970Aminoacyl-tRNA biosynthesis

Swiss-prot:Accession NumberP0A8M3Q8NW68
Entry nameSYT_ECOLISYT_STAAW
ActivityATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr).ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr).
SubunitHomodimer.Homodimer (By similarity).
Subcellular locationCytoplasm.Cytoplasm.
CofactorBinds 1 zinc ion per subunit.Binds 1 zinc ion per subunit (By similarity).


CofactorsSubstratesProductsintermediates
KEGG-idC00038C00305C00002C00188C01651C00013C00020C02992
CompoundZincMagnesiumATPL-ThreoninetRNA(Thr)PyrophosphateAMPL-Threonyl-tRNA(Thr)
Typeheavy metaldivalent metal (Ca2+, Mg2+)amine group,nucleotideamino acids,carbohydratenucleic acidsphosphate group/phosphate ionamine group,nucleotideamino acids,carbohydrate,nucleic acids
1qf6A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyqA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyqB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyrA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyrB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1qf6A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyqA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyqB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyrA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyrB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1qf6A03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyqA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyqB03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyrA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyrB03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1evkA01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1evkB01Bound:_ZNUnboundUnboundBound:THRUnboundUnboundUnboundUnboundUnbound
1evlA01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1evlB01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1evlC01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1evlD01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1fyfA01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:SSA
1fyfB01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:SSA
1kogA01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1kogB01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1kogC01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1kogD01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1kogE01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1kogF01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1kogG01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1kogH01Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1qf6A04Bound:_ZNUnboundUnboundUnboundBound:__A 76(chain B)UnboundBound:AMPUnboundUnbound
1nyqA04Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1nyqB04Bound:_ZNUnboundUnboundUnboundUnboundUnboundUnboundUnboundIntermediate-analogue:TSB
1nyrA04Bound:_ZNUnboundBound:ATPBound:THRUnboundUnboundUnboundUnboundUnbound
1nyrB04Bound:_ZNUnboundBound:ATPBound:THRUnboundUnboundUnboundUnboundUnbound
1evkA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1evkB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1evlA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1evlB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1evlC02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1evlD02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1fyfA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1fyfB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1kogA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1kogB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1kogC02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1kogD02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1kogE02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1kogF02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1kogG02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1kogH02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1qf6A05UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyqA05UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyqB05UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyrA05UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1nyrB05UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P0A8M3 & literature [3] & [13]
pdbCatalytic residuesCofactor-binding residues
1qf6A01

1nyqA01

1nyqB01

1nyrA01

1nyrB01

1qf6A02

1nyqA02

1nyqB02

1nyrA02

1nyrB02

1qf6A03

1nyqA03

1nyqB03

1nyrA03

1nyrB03

1evkA01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1evkB01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1evlA01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1evlB01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1evlC01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1evlD01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1fyfA01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1fyfB01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1kogA01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1kogB01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1kogC01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1kogD01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1kogE01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1kogF01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1kogG01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1kogH01ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1qf6A04ARG 363;ARG 375;LYS 465
CYS 334;HIS 385;HIS 511(Zinc binding);GLU 365(Magnesium binding)
1nyqA04ARG 365;ARG 377;LYS 471
CYS 336;HIS 387;HIS 517(Zinc binding);GLU 367(Magnesium binding)
1nyqB04ARG 365;ARG 377;LYS 471
CYS 336;HIS 387;HIS 517(Zinc binding);GLU 367(Magnesium binding)
1nyrA04ARG 365;ARG 377;LYS 471
CYS 336;HIS 387;HIS 517(Zinc binding);GLU 367(Magnesium binding)
1nyrB04ARG 365;ARG 377;LYS 471
CYS 336;HIS 387;HIS 517(Zinc binding);GLU 367(Magnesium binding)
1evkA02

1evkB02

1evlA02

1evlB02

1evlC02

1evlD02

1fyfA02

1fyfB02

1kogA02

1kogB02

1kogC02

1kogD02

1kogE02

1kogF02

1kogG02

1kogH02

1qf6A05

1nyqA05

1nyqB05

1nyrA05

1nyrB05


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[7]Fig.1, p.435
[13]p.206-207

references
[1]
PubMed ID2388270
JournalJ Mol Biol
Year1990
Volume214
Pages819-20
AuthorsGarber MB, Yaremchuk AD, Tukalo MA, Egorova SP, Fomenkova NP, Nikonov SV
TitleCrystals of threonyl-tRNA synthetase from Thermus thermophilus. Preliminary crystallographic data.
[2]
PubMed ID7589494
JournalFEBS Lett
Year1995
Volume374
Pages110-2
AuthorsCura V, Kern D, Mitschler A, Moras D
TitleCrystallization of threonyl-tRNA synthetase from Thermus thermophilus and preliminary crystallographic data.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
Medline ID99251535
PubMed ID10319817
JournalCell
Year1999
Volume97
Pages371-81
AuthorsSankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D
TitleThe structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site.
Related PDB1qf6
Related Swiss-protP0A8M3
[4]
CommentsX-ray crystallography
PubMed ID11136973
JournalCell
Year2000
Volume103
Pages877-84
AuthorsDock-Bregeon A, Sankaranarayanan R, Romby P, Caillet J, Springer M, Rees B, Francklyn CS, Ehresmann C, Moras D
TitleTransfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem.
Related PDB1fyf
[5]
PubMed ID10675344
JournalEMBO J
Year2000
Volume19
Pages749-57
AuthorsStaker BL, Korber P, Bardwell JC, Saper MA
TitleStructure of Hsp15 reveals a novel RNA-binding motif.
[6]
PubMed ID10632708
JournalEur J Biochem
Year2000
Volume267
Pages379-93
AuthorsCura V, Moras D, Kern D
TitleSequence analysis and modular organization of threonyl-tRNA synthetase from Thermus thermophilus and its interrelation with threonyl-tRNA synthetases of other origins.
[7]
PubMed ID10881182
JournalNat Struct Biol
Year2000
Volume7
Pages435-6
AuthorsMusier-Forsyth K, Beuning PJ
TitleRole of zinc ion in translational accuracy becomes crystal clear.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 242-642.
Medline ID20343005
PubMed ID10881191
JournalNat Struct Biol
Year2000
Volume7
Pages461-5
AuthorsSankaranarayanan R, Dock-Bregeon AC, Rees B, Bovee M, Caillet J, Romby P, Francklyn CS, Moras D
TitleZinc ion mediated amino acid discrimination by threonyl-tRNA synthetase.
Related PDB1evk,1evl
Related Swiss-protP0A8M3
[9]
PubMed ID11732604
JournalActa Biochim Pol
Year2001
Volume48
Pages323-35
AuthorsSankaranarayanan R, Moras D
TitleThe fidelity of the translation of the genetic code.
[10]
PubMed ID11953757
JournalNat Struct Biol
Year2002
Volume9
Pages343-7
AuthorsTorres-Larios A, Dock-Bregeon AC, Romby P, Rees B, Sankaranarayanan R, Caillet J, Springer M, Ehresmann C, Ehresmann B, Moras D
TitleStructural basis of translational control by Escherichia coli threonyl tRNA synthetase.
Related PDB1kog
[11]
PubMed ID14690420
JournalBiochemistry
Year2003
Volume42
Pages15102-13
AuthorsBovee ML, Pierce MA, Francklyn CS
TitleInduced fit and kinetic mechanism of adenylation catalyzed by Escherichia coli threonyl-tRNA synthetase.
[12]
PubMed ID12554667
JournalEMBO J
Year2003
Volume22
Pages668-75
AuthorsBeebe K, Ribas De Pouplana L, Schimmel P
TitleElucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viability.
[13]
PubMed ID12875846
JournalJ Mol Biol
Year2003
Volume331
Pages201-11
AuthorsTorres-Larios A, Sankaranarayanan R, Rees B, Dock-Bregeon AC, Moras D
TitleConformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase.
Related PDB1nyr
[14]
PubMed ID12581352
JournalMol Microbiol
Year2003
Volume47
Pages961-74
AuthorsCaillet J, Nogueira T, Masquida B, Winter F, Graffe M, Dock-Bregeon AC, Torres-Larios A, Sankaranarayanan R, Westhof E, Ehresmann B, Ehresmann C, Romby P, Springer M
TitleThe modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression.

comments
This enzyme belongs to the class-IIa aminoacyl-tRNA synthetase family.
Although the tertiary structures with magnesium ions have not been determined yet, Mg2+ ion might be bound to Glu365 (of 1evk), according to the paper [13].
According to the literature [7] & [8], zinc ion is involved in threonine recognition, discriminating it from other amino acids.
According to the literature [13], this enzyme catalyzes two successive transfer reactions. Firstly, it transfers the adenylate from ATP (the first substrate) to the carboxylate of the second substrate, threonine, resulting in the formation of threonyl-adenylate (intermediate) and the release of the inorganic pyrophosphate. Secondly, it transfers the acyl group from the intermediate to the 3'-OH of tRNA(Thr).
The first transfer reaction proceeds as follows (see [13]):
(1) The first substrate, ATP, adopts a bent conformation so that the alpha-phosphate group faces the carboxylate of the threonine.
(2) Arg363 stabilizes the negatively charged groups, the acceptor group (the carboxylate) and the transferred group (apha-phosphate of ATP), by neutralizing the charged groups. A magnesium ion coordinated to Glu365 also stabilizes the leaving group, the beta- and gamma-phosphphate moieties (or pyrophosphate).
(3) The stabilization of the negatively charged groups leads to an in-line nucleophilic attack by the carboxylate group on the alpha-phosphorus atom, by associative mechanism (SN2-like mechanism).
(4) The pentacovalent transition state is stabilized by three basic residues (Arg363, Arg375 & Lys465), and the magnesium ion. Here, the leaving group, the pyrophosphate, is stabilized by the magnesium ion, Arg375 and Lys465.
(5) The leaving group, the inorganic pyrophosphate, leaves the active site, probably together with the two bridging magnesium ions.
The second acyl transfer reaction has not been elucidated yet.

createdupdated
2004-10-252009-04-03
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 2010)
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)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.