DB code: T00106

CATH domain 3.40.50.620 : Rossmann fold Catalytic domain
1.10.730.10 : Isoleucyl-tRNA Synthetase; Domain 1
3.30.1360.70 : Gyrase A; domain 2
E.C. 6.1.1.19
CSA
M-CSA
MACiE M0235

CATH domain Related DB codes (homologues)
1.10.730.10 : Isoleucyl-tRNA Synthetase; Domain 1 M00177
3.40.50.620 : Rossmann fold S00314 S00549 S00316 S00317 S00318 S00315 T00085 T00249 D00300 M00177 M00178 T00114

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
Q05506 Arginyl-tRNA synthetase, cytoplasmic
EC 6.1.1.19
Arginine--tRNA ligase
ArgRS
NP_010628.3 (Protein)
NM_001180649.3 (DNA/RNA sequence)
PF03485 (Arg_tRNA_synt_N)
PF05746 (DALR_1)
PF00750 (tRNA-synt_1d)
[Graphical View]
Q93RP5
Arginyl-tRNA synthetase
EC 6.1.1.19
PF03485 (Arg_tRNA_synt_N)
PF05746 (DALR_1)
PF00750 (tRNA-synt_1d)
[Graphical View]

KEGG enzyme name
arginine---tRNA ligase
arginyl-tRNA synthetase
arginyl-transfer ribonucleate synthetase
arginyl-transfer RNA synthetase
arginyl transfer ribonucleic acid synthetase
arginine-tRNA synthetase
arginine translase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q05506 SYRC_YEAST ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg). Monomer. Cytoplasm.
Q93RP5 Q93RP5_THETH ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg). Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00330 Arginine and proline metabolism
MAP00970 Aminoacyl-tRNA biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00062 C01636 C00020 C00013 C02163
E.C.
Compound Magnesium ATP L-Arginine tRNA(Arg) AMP Pyrophosphate L-Arginyl-tRNA(Arg)
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide amino acids,amine group,imine group,lipid nucleic acids amine group,nucleotide phosphate group/phosphate ion amino acids,amine group,imine group,lipid,nucleic acids
ChEBI 18420
15422
16467
16027
29888
PubChem 888
5957
28782
6322
6083
1023
21961011
1bs2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ARG Unbound Unbound Unbound Unbound
1f7uA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:ARG Bound:__G-__C-__C-__A_976 (chain B) Unbound Unbound Unbound
1f7vA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:__G_973 (chain B) Unbound Unbound Unbound
1iq0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bs2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f7uA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f7vA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iq0A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bs2A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f7uA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f7vA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iq0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [11], [13] & [17]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bs2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 153;LYS 156;HIS 159;HIS 162;GLU 294;GLN 375
1f7uA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 153;LYS 156;HIS 159;HIS 162;GLU 294;GLN 375
1f7vA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 153;LYS 156;HIS 159;HIS 162;GLU 294;GLN 375
1iq0A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 113;LYS 116;HIS 119;HIS 122;GLU 240;GLN 357
1bs2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1f7uA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1f7vA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1iq0A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1bs2A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1f7uA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1f7vA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1iq0A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[11]
p.5443-5445
[13]
p.5606, p.5608-5609
[17]
p.3724-3725

References
[1]
Resource
Comments
Medline ID
PubMed ID 1253985
Journal FEBS Lett
Year 1976
Volume 62
Pages 190-3
Authors Godeau JM
Title Arginyl-tRNA synthetase from Bacillus stearothermophilus: subunit structure of enzyme.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 679950
Journal Eur J Biochem
Year 1978
Volume 87
Pages 583-90
Authors Carias JR, Mouricout M, Quintard B, Thomes JC, Julien R
Title Leucyl-tRNA and arginyl-tRNA synthetases of wheat germ: inactivation and ribosome effects.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 220092
Journal FEBS Lett
Year 1979
Volume 99
Pages 25-8
Authors Gerlo E, Charlier J
Title Irreversible inactivation of arginyl-tRNA ligase by periodate-oxidized tRNA.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 6273159
Journal Eur J Biochem
Year 1981
Volume 119
Pages 477-82
Authors Freist W, Sternbach H, Cramer F
Title Arginyl-tRNA synthetase from Baker's yeast. Order of substrate addition and action of ATP analogs in the aminoacylation reaction; influence of pyrophosphate on the catalytic mechanism.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7042510
Journal Hoppe Seylers Z Physiol Chem
Year 1982
Volume 363
Pages 365-73
Authors Gerlo E, Freist W, Charlier J
Title Arginyl-tRNA synthetase from Escherichia coli K12: specificity with regard to ATP analogs and their magnesium complexes.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 1953742
Journal Biochem Biophys Res Commun
Year 1991
Volume 180
Pages 702-8
Authors Huang S, Deutscher MP
Title The NH2-terminal extension of rat liver arginyl-tRNA synthetase is responsible for its hydrophobic properties.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 8224869
Journal Gene
Year 1993
Volume 132
Pages 237-45
Authors Lazard M, Mirande M
Title Cloning and analysis of a cDNA encoding mammalian arginyl-tRNA synthetase, a component of the multisynthetase complex with a hydrophobic N-terminal extension.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9396794
Journal Nucleic Acids Res
Year 1997
Volume 25
Pages 4899-906
Authors Sissler M, Eriani G, Martin F, Giege R, Florentz C
Title Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 9416614
Journal Protein Sci
Year 1997
Volume 6
Pages 2636-8
Authors Zhou M, Wang ED, Campbell RL, Wang YL, Lin SX
Title Crystallization and preliminary X-ray diffraction analysis of arginyl-tRNA synthetase from Escherichia coli.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 9748544
Journal Biochim Biophys Acta
Year 1998
Volume 1387
Pages 136-42
Authors Zhang QS, Wang ED, Wang YL
Title The role of tryptophan residues in Escherichia coli arginyl-tRNA synthetase.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS)
Medline ID 98409547
PubMed ID 9736621
Journal EMBO J
Year 1998
Volume 17
Pages 5438-48
Authors Cavarelli J, Delagoutte B, Eriani G, Gangloff J, Moras D
Title L-arginine recognition by yeast arginyl-tRNA synthetase.
Related PDB 1bs2
Related UniProtKB Q05506
[12]
Resource
Comments
Medline ID
PubMed ID 10333292
Journal J Protein Chem
Year 1999
Volume 18
Pages 187-92
Authors Zhang QS, Shen L, Wang ED, Wang YL
Title Biosynthesis and characterization of 4-fluorotryptophan-labeled Escherichia coli arginyl-tRNA synthetase.
Related PDB
Related UniProtKB
[13]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11060012
Journal EMBO J
Year 2000
Volume 19
Pages 5599-610
Authors Delagoutte B, Moras D, Cavarelli J
Title tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding.
Related PDB 1f7u 1f7v
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10993737
Journal J Mol Biol
Year 2000
Volume 302
Pages 991-1004
Authors Lazard M, Agou F, Kerjan P, Mirande M
Title The tRNA-dependent activation of arginine by arginyl-tRNA synthetase requires inter-domain communication.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10744027
Journal RNA
Year 2000
Volume 6
Pages 434-48
Authors Geslain R, Martin F, Delagoutte B, Cavarelli J, Gangloff J, Eriani G
Title In vivo selection of lethal mutations reveals two functional domains in arginyl-tRNA synthetase.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11733016
Journal Eur J Biochem
Year 2001
Volume 268
Pages 6207-13
Authors Kiga D, Sakamoto K, Sato S, Hirao I, Yokoyama S
Title Shifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11106639
Journal J Biol Chem
Year 2001
Volume 276
Pages 3723-6
Authors Sekine S, Shimada A, Nureki O, Cavarelli J, Moras D, Vassylyev DG, Yokoyama S
Title Crucial role of the high-loop lysine for the catalytic activity of arginyl-tRNA synthetase.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11717415
Journal Proc Natl Acad Sci U S A
Year 2001
Volume 98
Pages 13473-5
Authors Hendrickson TL
Title Recognizing the D-loop of transfer RNAs.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11698642
Journal Proc Natl Acad Sci U S A
Year 2001
Volume 98
Pages 13537-42
Authors Shimada A, Nureki O, Goto M, Takahashi S, Yokoyama S
Title Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase.
Related PDB 1iq0 1ir4
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 14690419
Journal Biochemistry
Year 2003
Volume 42
Pages 15092-101
Authors Geslain R, Bey G, Cavarelli J, Eriani G
Title Limited set of amino acid residues in a class Ia aminoacyl-tRNA synthetase is crucial for tRNA binding.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 12860413
Journal FEBS Lett
Year 2003
Volume 547
Pages 197-200
Authors Yao YN, Zhang QS, Yan XZ, Zhu G, Wang ED
Title Substrate-induced conformational changes in Escherichia coli arginyl-tRNA synthetase observed by 19F NMR spectroscopy.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 14672708
Journal Biochem Biophys Res Commun
Year 2004
Volume 313
Pages 129-34
Authors Yao YN, Zhang QS, Yan XZ, Zhu G, Wang ED
Title Escherichia coli tRNA(4)(Arg)(UCU) induces a constrained conformation of the crucial Omega-loop of arginyl-tRNA synthetase.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to class-I aminoacyl-tRNA synthetase family.
Although the tertiary structures with magnesium ions have not been determined yet, Mg2+ ions are required for the first step of catalysis, according to the paper [13].
According to the literature [11] and [13], this enzyme catalyzes two successive transfer reactions.
(A) Transfer of the adenylate from ATP (the first substrate) to the carboxylate of the second substrate, arginine: This reaction results in the formation of arginyl-adenylate (intermediate) and the release of the inorganic pyrophosphate.
(B) Transfer of the acyl group from the intermediate to the 2'-OH of tRNA(Arg).
The detailed catalytic mechanism has not been elucidated yet, though.

Created Updated
2004-09-14 2012-06-25