EzCatDB: D00291
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DB codeD00291
RLCP classification3.113.90030.330 : Transfer
CATH domainDomain 12.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 23.30.930.10 : BirA Bifunctional Protein; domain 2Catalytic domain
E.C.6.1.1.6

CATH domainRelated DB codes (homologues)
2.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)M00220,M00186,T00050,D00294,T00254
3.30.930.10 : BirA Bifunctional Protein; domain 2S00413,D00293,D00294,D00295,M00049,T00113

Enzyme Name
UniProtKBKEGG

P0A8N3P0A8N5
Protein nameLysyl-tRNA synthetaseLysyl-tRNA synthetase, heat induciblelysine---tRNA ligase
lysyl-tRNA synthetase
lysyl-transfer ribonucleate synthetase
lysyl-transfer RNA synthetase
L-lysine-transfer RNA ligase
lysine-tRNA synthetase
lysine translase
SynonymsEC 6.1.1.6
Lysine--tRNA ligase
LysRS
EC 6.1.1.6
Lysine--tRNA ligase
LysRS
RefSeqNP_417366.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491091.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
NP_418553.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492273.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF00152 (tRNA-synt_2)
PF01336 (tRNA_anti)
[Graphical view]
PF00152 (tRNA-synt_2)
PF01336 (tRNA_anti)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00300Lysine biosynthesis
MAP00970Aminoacyl-tRNA biosynthesis

UniProtKB:Accession NumberP0A8N3P0A8N5
Entry nameSYK1_ECOLISYK2_ECOLI
ActivityATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).
SubunitHomodimer.Homodimer.
Subcellular locationCytoplasm.Cytoplasm.
CofactorBinds 3 magnesium ions per subunit (By similarity).Binds 3 magnesium ions per subunit. The third one is coordinated by ATP.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00305C00002C00047C01646C00020C00013C01931
CompoundMagnesiumATPL-LysinetRNA(Lys)AMPPyrophosphateL-Lysyl-tRNA(Lys)Lysyl-adenylate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamino acids,amine group,lipidnucleic acidsamine group,nucleotidephosphate group/phosphate ionamino acids,amine group,lipid,nucleic acids
ChEBI18420
15422
18019

16027
29888


PubChem888
5957
71774817
5962

6083
21961011
1023


                
1bbuA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1bbwA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1e1oA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1e1tA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1e22A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1e24A01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1krsAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1krtAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1lylA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1lylB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1lylC01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1bbuA02UnboundUnboundBound:LYSUnboundUnboundUnboundUnboundUnbound
1bbwA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1e1oA02UnboundUnboundBound:LYSUnboundUnboundUnboundUnboundUnbound
1e1tA02Bound:2x_MGUnboundUnboundUnboundUnboundBound:POPUnboundIntermediate-bound:LAD
1e22A02Bound:3x_MGAnalogue:ACPBound:LYSUnboundUnboundUnboundUnboundUnbound
1e24A02Analogue:3x_MNBound:ATPBound:LYSUnboundUnboundUnboundUnboundUnbound
1lylA02UnboundUnboundBound:LYSUnboundUnboundUnboundUnboundUnbound
1lylB02UnboundUnboundBound:LYSUnboundUnboundUnboundUnboundUnbound
1lylC02UnboundUnboundBound:LYSUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P0A8N5, P0A8N3 & literature [8], [13]
pdbCatalytic residuesCofactor-binding residues
          
1bbuA01 
 
1bbwA01 
 
1e1oA01 
 
1e1tA01 
 
1e22A01 
 
1e24A01 
 
1krsA 
 
1krtA 
 
1lylA01 
 
1lylB01 
 
1lylC01 
 
1bbuA02ARG 262;HIS 270;ARG 480
GLU 414;GLU 421(Magnesium binding)
1bbwA02ARG 262;HIS 270;ARG 480
GLU 414;GLU 421(Magnesium binding)
1e1oA02ARG 262;HIS 270;ARG 480
GLU 414;GLU 421(Magnesium binding)
1e1tA02ARG 262;HIS 270;ARG 480
GLU 414;GLU 421(Magnesium binding)
1e22A02ARG 262;HIS 270;ARG 480
GLU 414;GLU 421(Magnesium binding)
1e24A02ARG 262;HIS 270;ARG 480
GLU 414;GLU 421(Manganese binding)
1lylA02ARG 262;HIS 270;ARG 480
GLU 414;GLU 421(Magnesium binding)
1lylB02ARG 262;HIS 270;ARG 480
GLU 414;GLU 421(Magnesium binding)
1lylC02ARG 262;HIS 270;ARG 480
GLU 414;GLU 421(Magnesium binding)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[8]p.170-171
[13]p.8422-8424
[14]p.12855-12856
[17]


references
[1]
PubMed ID6277395
JournalBiochimie
Year1981
Volume63
Pages827-30
AuthorsPlateau P, Gueron M, Blanquet S
TitleDetermination of dinucleoside 5', 5"'-P1, P4- tetraphosphates by 31P and 1H NMR spectroscopy.
[2]
PubMed ID6756470
JournalBiochemistry
Year1982
Volume21
Pages5273-9
AuthorsPlateau P, Blanquet S
TitleZinc-dependent synthesis of various dinucleoside 5',5' ' '-P1,P3-Tri- or 5'',5' ' '-P1,P4-tetraphosphates by Escherichia coli lysyl-tRNA synthetase.
[3]
PubMed ID2496111
JournalJ Bacteriol
Year1989
Volume171
Pages2619-25
AuthorsMatthews RG, Neidhardt FC
TitleElevated serine catabolism is associated with the heat shock response in Escherichia coli.
[4]
PubMed ID7932734
JournalJ Mol Biol
Year1994
Volume243
Pages123-5
AuthorsOnesti S, Theoclitou ME, Pernilla E, Wittung L, Miller AD, Plateau P, Blanquet S, Brick P
TitleCrystallization and preliminary diffraction studies of Escherichia coli lysyl-tRNA synthetase (LysU).
[5]
PubMed ID7794932
JournalBiochemistry
Year1995
Volume34
Pages8180-9
AuthorsCommans S, Blanquet S, Plateau P
TitleA single substitution in the motif 1 of Escherichia coli lysyl-tRNA synthetase induces cooperativity toward amino acid binding.
[6]
CommentsNMR Structure
PubMed ID7473706
JournalJ Mol Biol
Year1995
Volume253
Pages100-13
AuthorsCommans S, Plateau P, Blanquet S, Dardel F
TitleSolution structure of the anticodon-binding domain of Escherichia coli lysyl-tRNA synthetase and studies of its interaction with tRNA(Lys).
Related PDB1krs,1krt
[7]
PubMed ID7540304
JournalProteins
Year1995
Volume21
Pages261-4
AuthorsYaremchuk AD, Krikliviy IA, Cusack S, Tukalo MA
TitleCocrystallization of lysyl-tRNA synthetase from Thermus thermophilus with its cognate tRNAlys and with Escherichia coli tRNAlys.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
Medline ID95253817
PubMed ID7735833
JournalStructure
Year1995
Volume3
Pages163-76
AuthorsOnesti S, Miller AD, Brick P
TitleThe crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli.
Related PDB1lyl
Related UniProtKBP0A8N5
[9]
PubMed ID9287150
JournalBiochemistry
Year1997
Volume36
Pages11077-85
AuthorsJakubowski H
TitleAminoacyl thioester chemistry of class II aminoacyl-tRNA synthetases.
[10]
PubMed ID9614943
JournalJ Mol Biol
Year1998
Volume278
Pages801-13
AuthorsCommans S, Lazard M, Delort F, Blanquet S, Plateau P
TitletRNA anticodon recognition and specification within subclass IIb aminoacyl-tRNA synthetases.
[11]
PubMed ID9525626
JournalJ Virol
Year1998
Volume72
Pages3037-44
AuthorsStark LA, Hay RT
TitleHuman immunodeficiency virus type 1 (HIV-1) viral protein R (Vpr) interacts with Lys-tRNA synthetase: implications for priming of HIV-1 reverse transcription.
[12]
PubMed ID10369781
JournalJ Mol Biol
Year1999
Volume289
Pages1041-54
AuthorsAlexandrescu AT, Jaravine VA, Dames SA, Lamour FP
TitleNMR hydrogen exchange of the OB-fold protein LysN as a function of denaturant: the most conserved elements of structure are the most stable to unfolding.
[13]
CommentsX-RAY CRYSTALLOGRAPHY (2.12 ANGSTROMS).
Medline ID20374515
PubMed ID10913247
JournalBiochemistry
Year2000
Volume39
Pages8418-25
AuthorsDesogus G, Todone F, Brick P, Onesti S
TitleActive site of lysyl-tRNA synthetase: structural studies of the adenylation reaction.
Related PDB1e1o,1e1t,1e22,1e24
Related UniProtKBP0A8N5
[14]
CommentsX-ray crystallography
PubMed ID11041850
JournalBiochemistry
Year2000
Volume39
Pages12853-61
AuthorsOnesti S, Desogus G, Brevet A, Chen J, Plateau P, Blanquet S, Brick P
TitleStructural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding.
Related PDB1bbu,1bbw
[15]
PubMed ID10623523
JournalJ Mol Biol
Year2000
Volume295
Pages239-55
AuthorsAlexandrescu AT, Lamour FP, Jaravine VA
TitleNMR evidence for progressive stabilization of native-like structure upon aggregation of acid-denatured LysN.
[16]
PubMed ID11706011
JournalJ Biol Chem
Year2002
Volume277
Pages1762-9
AuthorsFrancin M, Kaminska M, Kerjan P, Mirande M
TitleThe N-terminal domain of mammalian Lysyl-tRNA synthetase is a functional tRNA-binding domain.
[17]
PubMed ID12019264
JournalJ Biol Chem
Year2002
Volume277
Pages29275-82
AuthorsTakita T, Inouye K
TitleTransition state stabilization by the N-terminal anticodon-binding domain of lysyl-tRNA synthetase.
[18]
PubMed ID11887185
JournalNat Struct Biol
Year2002
Volume9
Pages257-62
AuthorsTerada T, Nureki O, Ishitani R, Ambrogelly A, Ibba M, Soll D, Yokoyama S
TitleFunctional convergence of two lysyl-tRNA synthetases with unrelated topologies.
[19]
PubMed ID12787471
JournalBMC Struct Biol
Year2003
Volume3
Pages5
AuthorsHughes SJ, Tanner JA, Hindley AD, Miller AD, Gould IR
TitleFunctional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment.
[20]
PubMed ID12507472
JournalJ Mol Biol
Year2003
Volume325
Pages677-95
AuthorsTakita T, Nakagoshi M, Inouye K, Tonomura B
TitleLysyl-tRNA synthetase from Bacillus stearothermophilus: the Trp314 residue is shielded in a non-polar environment and is responsible for the fluorescence changes observed in the amino acid activation reaction.

comments
This enzyme belongs to the class-IIb aminoacyl-tRNA synthetase family.
This enzyme catalyzes two successive transfer reactions. Firstly, it transfers the adenylate from ATP (the first substrate) to the carboxylate of the second substrate, lysine, resulting in the formation of lysyl-adenylate (intermediate) and the release of the inorganic pyrophosphate. Secondly, it transfers the acyl group from the intermediate to the 3'-OH of tRNA(Lys).
(A) The first transfer reaction of phosphoryl group proceeds as follows (see [8], [13] & [14]):
(A1) The first substrate, ATP, adopts a bent conformation so that the alpha-phosphate group faces the carboxylate of the second substrate, lysine, for the nucleophilic attack.
(A2) Arg262 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 Glu414 and Glu421 also stabilizes the transferred group, the alpha-phosphate moiety, and the leaving group, the beta-phosphate group.
(A3) 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).
(A4) The pentacovalent transition state is stabilized by Arg262, and the above magnesium ion. Here, the leaving group, the pyrophosphate, is stabilized by the three magnesium ions, along with His270 and Arg480.
(A5) The leaving group, the inorganic pyrophosphate, leaves the active site, together with the two bridging magnesium ions.
(B) The second acyl transfer reaction has not been elucidated yet.

createdupdated
2004-09-272009-02-26


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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)
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