DB code: D00291

RLCP classification 3.113.90030.330 : Transfer
CATH domain 2.40.50.140 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
3.30.930.10 : BirA Bifunctional Protein; domain 2 Catalytic domain
E.C. 6.1.1.6
CSA
M-CSA
MACiE

CATH domain Related 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 2 S00413 D00293 D00294 D00295 M00049 T00113

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0A8N3 Lysyl-tRNA synthetase
EC 6.1.1.6
Lysine--tRNA ligase
LysRS
NP_417366.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491091.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00152 (tRNA-synt_2)
PF01336 (tRNA_anti)
[Graphical View]
P0A8N5 Lysyl-tRNA synthetase, heat inducible
EC 6.1.1.6
Lysine--tRNA ligase
LysRS
NP_418553.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492273.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF00152 (tRNA-synt_2)
PF01336 (tRNA_anti)
[Graphical View]

KEGG enzyme name
lysine---tRNA ligase
lysyl-tRNA synthetase
lysyl-transfer ribonucleate synthetase
lysyl-transfer RNA synthetase
L-lysine-transfer RNA ligase
lysine-tRNA synthetase
lysine translase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0A8N3 SYK1_ECOLI ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys). Homodimer. Cytoplasm. Binds 3 magnesium ions per subunit (By similarity).
P0A8N5 SYK2_ECOLI ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys). Homodimer. Cytoplasm. Binds 3 magnesium ions per subunit. The third one is coordinated by ATP.

KEGG Pathways
Map code Pathways E.C.
MAP00300 Lysine biosynthesis
MAP00970 Aminoacyl-tRNA biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00047 C01646 C00020 C00013 C01931
E.C.
Compound Magnesium ATP L-Lysine tRNA(Lys) AMP Pyrophosphate L-Lysyl-tRNA(Lys) Lysyl-adenylate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide amino acids,amine group,lipid nucleic acids amine group,nucleotide phosphate group/phosphate ion amino acids,amine group,lipid,nucleic acids
ChEBI 18420
15422
18019
16027
29888
PubChem 888
5957
5962
71774817
6083
1023
21961011
1bbuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bbwA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1e1oA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1e1tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1e22A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1e24A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1krsA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1krtA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1lylA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1lylB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1lylC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bbuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:LYS Unbound Unbound Unbound Unbound Unbound
1bbwA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1e1oA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:LYS Unbound Unbound Unbound Unbound Unbound
1e1tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Unbound Unbound Unbound Bound:POP Unbound Intermediate-bound:LAD
1e22A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_MG Analogue:ACP Bound:LYS Unbound Unbound Unbound Unbound Unbound
1e24A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:3x_MN Bound:ATP Bound:LYS Unbound Unbound Unbound Unbound Unbound
1lylA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:LYS Unbound Unbound Unbound Unbound Unbound
1lylB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:LYS Unbound Unbound Unbound Unbound Unbound
1lylC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:LYS Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P0A8N5, P0A8N3 & literature [8], [13]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bbuA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bbwA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1e1oA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1e1tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1e22A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1e24A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1krsA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1krtA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1lylA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1lylB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1lylC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bbuA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 262;HIS 270;ARG 480 GLU 414;GLU 421(Magnesium binding)
1bbwA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 262;HIS 270;ARG 480 GLU 414;GLU 421(Magnesium binding)
1e1oA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 262;HIS 270;ARG 480 GLU 414;GLU 421(Magnesium binding)
1e1tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 262;HIS 270;ARG 480 GLU 414;GLU 421(Magnesium binding)
1e22A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 262;HIS 270;ARG 480 GLU 414;GLU 421(Magnesium binding)
1e24A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 262;HIS 270;ARG 480 GLU 414;GLU 421(Manganese binding)
1lylA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 262;HIS 270;ARG 480 GLU 414;GLU 421(Magnesium binding)
1lylB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 262;HIS 270;ARG 480 GLU 414;GLU 421(Magnesium binding)
1lylC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 262;HIS 270;ARG 480 GLU 414;GLU 421(Magnesium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[8]
p.170-171
[13]
p.8422-8424
[14]
p.12855-12856
[17]

References
[1]
Resource
Comments
Medline ID
PubMed ID 6277395
Journal Biochimie
Year 1981
Volume 63
Pages 827-30
Authors Plateau P, Gueron M, Blanquet S
Title Determination of dinucleoside 5', 5"'-P1, P4- tetraphosphates by 31P and 1H NMR spectroscopy.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 6756470
Journal Biochemistry
Year 1982
Volume 21
Pages 5273-9
Authors Plateau P, Blanquet S
Title Zinc-dependent synthesis of various dinucleoside 5',5' ' '-P1,P3-Tri- or 5'',5' ' '-P1,P4-tetraphosphates by Escherichia coli lysyl-tRNA synthetase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2496111
Journal J Bacteriol
Year 1989
Volume 171
Pages 2619-25
Authors Matthews RG, Neidhardt FC
Title Elevated serine catabolism is associated with the heat shock response in Escherichia coli.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7932734
Journal J Mol Biol
Year 1994
Volume 243
Pages 123-5
Authors Onesti S, Theoclitou ME, Pernilla E, Wittung L, Miller AD, Plateau P, Blanquet S, Brick P
Title Crystallization and preliminary diffraction studies of Escherichia coli lysyl-tRNA synthetase (LysU).
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7794932
Journal Biochemistry
Year 1995
Volume 34
Pages 8180-9
Authors Commans S, Blanquet S, Plateau P
Title A single substitution in the motif 1 of Escherichia coli lysyl-tRNA synthetase induces cooperativity toward amino acid binding.
Related PDB
Related UniProtKB
[6]
Resource
Comments NMR Structure
Medline ID
PubMed ID 7473706
Journal J Mol Biol
Year 1995
Volume 253
Pages 100-13
Authors Commans S, Plateau P, Blanquet S, Dardel F
Title Solution structure of the anticodon-binding domain of Escherichia coli lysyl-tRNA synthetase and studies of its interaction with tRNA(Lys).
Related PDB 1krs 1krt
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 7540304
Journal Proteins
Year 1995
Volume 21
Pages 261-4
Authors Yaremchuk AD, Krikliviy IA, Cusack S, Tukalo MA
Title Cocrystallization of lysyl-tRNA synthetase from Thermus thermophilus with its cognate tRNAlys and with Escherichia coli tRNAlys.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
Medline ID 95253817
PubMed ID 7735833
Journal Structure
Year 1995
Volume 3
Pages 163-76
Authors Onesti S, Miller AD, Brick P
Title The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli.
Related PDB 1lyl
Related UniProtKB P0A8N5
[9]
Resource
Comments
Medline ID
PubMed ID 9287150
Journal Biochemistry
Year 1997
Volume 36
Pages 11077-85
Authors Jakubowski H
Title Aminoacyl thioester chemistry of class II aminoacyl-tRNA synthetases.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9614943
Journal J Mol Biol
Year 1998
Volume 278
Pages 801-13
Authors Commans S, Lazard M, Delort F, Blanquet S, Plateau P
Title tRNA anticodon recognition and specification within subclass IIb aminoacyl-tRNA synthetases.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9525626
Journal J Virol
Year 1998
Volume 72
Pages 3037-44
Authors Stark LA, Hay RT
Title Human immunodeficiency virus type 1 (HIV-1) viral protein R (Vpr) interacts with Lys-tRNA synthetase: implications for priming of HIV-1 reverse transcription.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10369781
Journal J Mol Biol
Year 1999
Volume 289
Pages 1041-54
Authors Alexandrescu AT, Jaravine VA, Dames SA, Lamour FP
Title NMR 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.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.12 ANGSTROMS).
Medline ID 20374515
PubMed ID 10913247
Journal Biochemistry
Year 2000
Volume 39
Pages 8418-25
Authors Desogus G, Todone F, Brick P, Onesti S
Title Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction.
Related PDB 1e1o 1e1t 1e22 1e24
Related UniProtKB P0A8N5
[14]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11041850
Journal Biochemistry
Year 2000
Volume 39
Pages 12853-61
Authors Onesti S, Desogus G, Brevet A, Chen J, Plateau P, Blanquet S, Brick P
Title Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding.
Related PDB 1bbu 1bbw
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10623523
Journal J Mol Biol
Year 2000
Volume 295
Pages 239-55
Authors Alexandrescu AT, Lamour FP, Jaravine VA
Title NMR evidence for progressive stabilization of native-like structure upon aggregation of acid-denatured LysN.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11706011
Journal J Biol Chem
Year 2002
Volume 277
Pages 1762-9
Authors Francin M, Kaminska M, Kerjan P, Mirande M
Title The N-terminal domain of mammalian Lysyl-tRNA synthetase is a functional tRNA-binding domain.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 12019264
Journal J Biol Chem
Year 2002
Volume 277
Pages 29275-82
Authors Takita T, Inouye K
Title Transition state stabilization by the N-terminal anticodon-binding domain of lysyl-tRNA synthetase.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11887185
Journal Nat Struct Biol
Year 2002
Volume 9
Pages 257-62
Authors Terada T, Nureki O, Ishitani R, Ambrogelly A, Ibba M, Soll D, Yokoyama S
Title Functional convergence of two lysyl-tRNA synthetases with unrelated topologies.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 12787471
Journal BMC Struct Biol
Year 2003
Volume 3
Pages 5
Authors Hughes SJ, Tanner JA, Hindley AD, Miller AD, Gould IR
Title Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 12507472
Journal J Mol Biol
Year 2003
Volume 325
Pages 677-95
Authors Takita T, Nakagoshi M, Inouye K, Tonomura B
Title Lysyl-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.
Related PDB
Related UniProtKB

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.

Created Updated
2004-09-27 2009-02-26