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
 18420
 		15422
 15422
 		16467
 16467
 		16027
 16027
 		29888
 29888
PubChem 888
 888
 		5957
 5957
 		28782
 6322
 28782
 6322
 		6083
 6083
 		1023
 21961011
 1023
 21961011
1bs2A01 Unbound Unbound Bound:ARG Unbound Unbound Unbound Unbound
1f7uA01 Unbound Unbound Bound:ARG Bound:__G-__C-__C-__A_976 (chain B) Unbound Unbound Unbound
1f7vA01 Unbound Unbound Unbound Analogue:__G_973 (chain B) Unbound Unbound Unbound
1iq0A01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bs2A02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f7uA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f7vA02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iq0A03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bs2A03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f7uA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1f7vA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iq0A02 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 ASN 153;LYS 156;HIS 159;HIS 162;GLU 294;GLN 375
1f7uA01 ASN 153;LYS 156;HIS 159;HIS 162;GLU 294;GLN 375
1f7vA01 ASN 153;LYS 156;HIS 159;HIS 162;GLU 294;GLN 375
1iq0A01 ASN 113;LYS 116;HIS 119;HIS 122;GLU 240;GLN 357
1bs2A02
1f7uA02
1f7vA02
1iq0A03
1bs2A03
1f7uA03
1f7vA03
1iq0A02

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