EzCatDB: T00106
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DB codeT00106
CATH domainDomain 13.40.50.620 : Rossmann foldCatalytic domain
Domain 21.10.730.10 : Isoleucyl-tRNA Synthetase; Domain 1
Domain 33.30.1360.70 : Gyrase A; domain 2
E.C.6.1.1.19
MACiEM0235

CATH domainRelated DB codes (homologues)
1.10.730.10 : Isoleucyl-tRNA Synthetase; Domain 1M00177
3.40.50.620 : Rossmann foldS00314,S00549,S00316,S00317,S00318,S00315,T00085,T00249,D00300,M00177,M00178,T00114

Enzyme Name
UniProtKBKEGG

Q05506Q93RP5
Protein nameArginyl-tRNA synthetase, cytoplasmic
arginine---tRNA ligase
arginyl-tRNA synthetase
arginyl-transfer ribonucleate synthetase
arginyl-transfer RNA synthetase
arginyl transfer ribonucleic acid synthetase
arginine-tRNA synthetase
arginine translase
SynonymsEC 6.1.1.19
Arginine--tRNA ligase
ArgRS
Arginyl-tRNA synthetase
EC 6.1.1.19
RefSeqNP_010628.3 (Protein)
NM_001180649.3 (DNA/RNA sequence)

PfamPF03485 (Arg_tRNA_synt_N)
PF05746 (DALR_1)
PF00750 (tRNA-synt_1d)
[Graphical view]
PF03485 (Arg_tRNA_synt_N)
PF05746 (DALR_1)
PF00750 (tRNA-synt_1d)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00330Arginine and proline metabolism
MAP00970Aminoacyl-tRNA biosynthesis

UniProtKB:Accession NumberQ05506Q93RP5
Entry nameSYRC_YEASTQ93RP5_THETH
ActivityATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg).ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg).
SubunitMonomer.
Subcellular locationCytoplasm.Cytoplasm.
Cofactor


Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00002C00062C01636C00020C00013C02163
CompoundMagnesiumATPL-ArgininetRNA(Arg)AMPPyrophosphateL-Arginyl-tRNA(Arg)
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotideamino acids,amine group,imine group,lipidnucleic acidsamine group,nucleotidephosphate group/phosphate ionamino acids,amine group,imine group,lipid,nucleic acids
ChEBI18420
15422
16467

16027
29888

PubChem888
5957
6322
28782

6083
21961011
1023

               
1bs2A01UnboundUnboundBound:ARGUnboundUnboundUnboundUnbound
1f7uA01UnboundUnboundBound:ARGBound:__G-__C-__C-__A 976(chain B)UnboundUnboundUnbound
1f7vA01UnboundUnboundUnboundAnalogue:__G 973(chain B)UnboundUnboundUnbound
1iq0A01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1bs2A02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1f7uA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1f7vA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1iq0A03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1bs2A03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1f7uA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1f7vA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1iq0A02UnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
literature [11], [13] & [17]
pdbCatalytic residues
         
1bs2A01ASN 153;LYS 156;HIS 159;HIS 162;GLU 294;GLN 375
1f7uA01ASN 153;LYS 156;HIS 159;HIS 162;GLU 294;GLN 375
1f7vA01ASN 153;LYS 156;HIS 159;HIS 162;GLU 294;GLN 375
1iq0A01ASN 113;LYS 116;HIS 119;HIS 122;GLU 240;GLN 357
1bs2A02 
1f7uA02 
1f7vA02 
1iq0A03 
1bs2A03 
1f7uA03 
1f7vA03 
1iq0A02 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[11]p.5443-5445
[13]p.5606, p.5608-5609
[17]p.3724-3725

references
[1]
PubMed ID1253985
JournalFEBS Lett
Year1976
Volume62
Pages190-3
AuthorsGodeau JM
TitleArginyl-tRNA synthetase from Bacillus stearothermophilus: subunit structure of enzyme.
[2]
PubMed ID679950
JournalEur J Biochem
Year1978
Volume87
Pages583-90
AuthorsCarias JR, Mouricout M, Quintard B, Thomes JC, Julien R
TitleLeucyl-tRNA and arginyl-tRNA synthetases of wheat germ: inactivation and ribosome effects.
[3]
PubMed ID220092
JournalFEBS Lett
Year1979
Volume99
Pages25-8
AuthorsGerlo E, Charlier J
TitleIrreversible inactivation of arginyl-tRNA ligase by periodate-oxidized tRNA.
[4]
PubMed ID6273159
JournalEur J Biochem
Year1981
Volume119
Pages477-82
AuthorsFreist W, Sternbach H, Cramer F
TitleArginyl-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.
[5]
PubMed ID7042510
JournalHoppe Seylers Z Physiol Chem
Year1982
Volume363
Pages365-73
AuthorsGerlo E, Freist W, Charlier J
TitleArginyl-tRNA synthetase from Escherichia coli K12: specificity with regard to ATP analogs and their magnesium complexes.
[6]
PubMed ID1953742
JournalBiochem Biophys Res Commun
Year1991
Volume180
Pages702-8
AuthorsHuang S, Deutscher MP
TitleThe NH2-terminal extension of rat liver arginyl-tRNA synthetase is responsible for its hydrophobic properties.
[7]
PubMed ID8224869
JournalGene
Year1993
Volume132
Pages237-45
AuthorsLazard M, Mirande M
TitleCloning and analysis of a cDNA encoding mammalian arginyl-tRNA synthetase, a component of the multisynthetase complex with a hydrophobic N-terminal extension.
[8]
PubMed ID9396794
JournalNucleic Acids Res
Year1997
Volume25
Pages4899-906
AuthorsSissler M, Eriani G, Martin F, Giege R, Florentz C
TitleMirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase.
[9]
PubMed ID9416614
JournalProtein Sci
Year1997
Volume6
Pages2636-8
AuthorsZhou M, Wang ED, Campbell RL, Wang YL, Lin SX
TitleCrystallization and preliminary X-ray diffraction analysis of arginyl-tRNA synthetase from Escherichia coli.
[10]
PubMed ID9748544
JournalBiochim Biophys Acta
Year1998
Volume1387
Pages136-42
AuthorsZhang QS, Wang ED, Wang YL
TitleThe role of tryptophan residues in Escherichia coli arginyl-tRNA synthetase.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS)
Medline ID98409547
PubMed ID9736621
JournalEMBO J
Year1998
Volume17
Pages5438-48
AuthorsCavarelli J, Delagoutte B, Eriani G, Gangloff J, Moras D
TitleL-arginine recognition by yeast arginyl-tRNA synthetase.
Related PDB1bs2
Related UniProtKBQ05506
[12]
PubMed ID10333292
JournalJ Protein Chem
Year1999
Volume18
Pages187-92
AuthorsZhang QS, Shen L, Wang ED, Wang YL
TitleBiosynthesis and characterization of 4-fluorotryptophan-labeled Escherichia coli arginyl-tRNA synthetase.
[13]
CommentsX-ray crystallography
PubMed ID11060012
JournalEMBO J
Year2000
Volume19
Pages5599-610
AuthorsDelagoutte B, Moras D, Cavarelli J
TitletRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding.
Related PDB1f7u,1f7v
[14]
PubMed ID10993737
JournalJ Mol Biol
Year2000
Volume302
Pages991-1004
AuthorsLazard M, Agou F, Kerjan P, Mirande M
TitleThe tRNA-dependent activation of arginine by arginyl-tRNA synthetase requires inter-domain communication.
[15]
PubMed ID10744027
JournalRNA
Year2000
Volume6
Pages434-48
AuthorsGeslain R, Martin F, Delagoutte B, Cavarelli J, Gangloff J, Eriani G
TitleIn vivo selection of lethal mutations reveals two functional domains in arginyl-tRNA synthetase.
[16]
PubMed ID11733016
JournalEur J Biochem
Year2001
Volume268
Pages6207-13
AuthorsKiga D, Sakamoto K, Sato S, Hirao I, Yokoyama S
TitleShifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase.
[17]
PubMed ID11106639
JournalJ Biol Chem
Year2001
Volume276
Pages3723-6
AuthorsSekine S, Shimada A, Nureki O, Cavarelli J, Moras D, Vassylyev DG, Yokoyama S
TitleCrucial role of the high-loop lysine for the catalytic activity of arginyl-tRNA synthetase.
[18]
PubMed ID11717415
JournalProc Natl Acad Sci U S A
Year2001
Volume98
Pages13473-5
AuthorsHendrickson TL
TitleRecognizing the D-loop of transfer RNAs.
[19]
PubMed ID11698642
JournalProc Natl Acad Sci U S A
Year2001
Volume98
Pages13537-42
AuthorsShimada A, Nureki O, Goto M, Takahashi S, Yokoyama S
TitleStructural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase.
Related PDB1iq0,1ir4
[20]
PubMed ID14690419
JournalBiochemistry
Year2003
Volume42
Pages15092-101
AuthorsGeslain R, Bey G, Cavarelli J, Eriani G
TitleLimited set of amino acid residues in a class Ia aminoacyl-tRNA synthetase is crucial for tRNA binding.
[21]
PubMed ID12860413
JournalFEBS Lett
Year2003
Volume547
Pages197-200
AuthorsYao YN, Zhang QS, Yan XZ, Zhu G, Wang ED
TitleSubstrate-induced conformational changes in Escherichia coli arginyl-tRNA synthetase observed by 19F NMR spectroscopy.
[22]
PubMed ID14672708
JournalBiochem Biophys Res Commun
Year2004
Volume313
Pages129-34
AuthorsYao YN, Zhang QS, Yan XZ, Zhu G, Wang ED
TitleEscherichia coli tRNA(4)(Arg)(UCU) induces a constrained conformation of the crucial Omega-loop of arginyl-tRNA synthetase.

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.

createdupdated
2004-09-142012-06-25
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 2008)
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)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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