Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: arginyl-tRNA synthetase



Gene: argS Accession Numbers: EG10071 (EcoCyc), b1876, ECK1877

Synonyms: lov, lov-1, ArgRS

Regulation Summary Diagram: ?

Summary:
Arginyl-tRNA synthetase (ArgRS) is a member of the family of aminoacyl tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis. ArgRS belongs to the Class IA aminoacyl tRNA synthetases; apart from sequence motifs within the active site, the different enzymes show little similarity in their primary amino acid sequences [Eriani90a, Landes95].

The kinetic mechanism of ArgRS has been investigated [Airas06].

ArgRS has been crystallized [Zhou97a, Zhou07], and the structure of a complex with L-arginine has been solved at 2.9 Å resolution, elucidating the structural and fuctional role of active site residues [Bi14a]. Conformational changes induced by interactions with its tRNA and arginine substrates have been studied [Yao04, Yao03, Gu96], and specific interations with nucleotide residues in some tRNA species have been determined [Kiga01].

Specificity determinants within tRNAArg that are important for recognition by ArgRS have been identified [Chakraburtty80, Schulman89, McClain90, Tamura92, Kiga01, Aldinger12].

The argS open reading frame uses the unusual initiation codon GUG and has a codon usage pattern which is typical for highly expressed genes [Eriani89]. Several mutations in argS have been described. The MA5002 mutant carries an Arg134Ser mutation located close to the active site of ArgRS, leading to defects in enzymatic activity and Km value for ATP [Eriani90b]. The lov-1 mutation confers a slow growth phenotype as well as mecillinam resistance, which appears to be dependent on the RelA-mediated stringent response [Vinella92]. An argS mutant conferring novobiocin resistance has been isolated [Jovanovic99a]. Site-directed and random mutagenesis has enabled identification of a variety of residues that are important for enzymatic activity [Zhang98e, Liu99d, Wu98, Kiga01, Bi14a].

ArgRS levels are unaffected by the level of arginine in the growth medium [Kryzek76].

Reviews: [Giege12, Perona12]

Citations: [Hirshfield68, Yem71, Faanes72, Charlier76a, Lui78, Neidhardt77, Reeh77, Gerlo82, Cooper69a, Mitra67, Mehler67, Cheng91, Jakubowski95, Airas96, Zhang99, Liu00, Liu01, Liu02a, Liu99e, Wu98a]

Locations: cytosol

Map Position: [1,958,086 -> 1,959,819] (42.2 centisomes)
Length: 1734 bp / 577 aa

Molecular Weight of Polypeptide: 64.683 kD (from nucleotide sequence), 60.0 kD (experimental) [Godeau79 ]

Unification Links: ASAP:ABE-0006264 , CGSC:1010 , DIP:DIP-9147N , EchoBASE:EB0069 , EcoGene:EG10071 , EcoliWiki:b1876 , Mint:MINT-1241236 , ModBase:P11875 , OU-Microarray:b1876 , PortEco:argS , PR:PRO_000022135 , Pride:P11875 , Protein Model Portal:P11875 , RefSeq:NP_416390 , RegulonDB:EG10071 , SMR:P11875 , String:511145.b1876 , UniProt:P11875

Relationship Links: InterPro:IN-FAMILY:IPR001278 , InterPro:IN-FAMILY:IPR001412 , InterPro:IN-FAMILY:IPR005148 , InterPro:IN-FAMILY:IPR008909 , InterPro:IN-FAMILY:IPR009080 , InterPro:IN-FAMILY:IPR014729 , InterPro:IN-FAMILY:IPR015945 , Panther:IN-FAMILY:PTHR11956 , PDB:Structure:4OBY , Pfam:IN-FAMILY:PF00750 , Pfam:IN-FAMILY:PF03485 , Pfam:IN-FAMILY:PF05746 , Prints:IN-FAMILY:PR01038 , Prosite:IN-FAMILY:PS00178 , Smart:IN-FAMILY:SM00836 , Smart:IN-FAMILY:SM01016

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006420 - arginyl-tRNA aminoacylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Charlier79]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11]
GO:0006418 - tRNA aminoacylation for protein translation Inferred by computational analysis [GOA01a]
Molecular Function: GO:0004814 - arginine-tRNA ligase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Charlier79]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01a]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01a]

MultiFun Terms: information transfer protein related amino acid -activation

Essentiality data for argS knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Credits:
Last-Curated ? 22-Apr-2014 by Keseler I , SRI International


Enzymatic reaction of: arginyl-tRNA synthetase

Synonyms: arginine--tRNA ligase

EC Number: 6.1.1.19

tRNAarg + L-arginine + ATP + H+ <=> L-arginyl-tRNAarg + AMP + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for ATP: dATP [Hirshfield69 ]

In Pathways: tRNA charging

Summary:
One molecule of ATP is utilized per aminoacylation reaction [Godeau79, Charlier79].

Citations: [Lin88b]

Cofactors or Prosthetic Groups: Mg2+ [Charlier79, Hirshfield69, Airas96]

Inhibitors (Competitive): homoarginine (Kic = 2400µM) [Charlier79] , L-canavanine (Kic = 300µM) [Hirshfield69]

Inhibitors (Noncompetitive): AMP (Ki = 1600µM) [Charlier79] , diphosphate (Ki = 100µM) [Charlier79]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
tRNAarg
3.0
[Zhang99, BRENDA14]
tRNAarg
2.5
[Lin88a]
tRNAarg
1.0
17.0
[Kiga01, BRENDA14]
tRNAarg
1.9
2.0, 21.9
[Yao04, BRENDA14]
L-arginine
150.0
[Gerlo82, BRENDA14]
L-arginine
9.0, 110.0, 700.0
[Eriani90b, BRENDA14]
L-arginine
12.0
[Zhang98e, BRENDA14]
L-arginine
13.7, 12.0
[Zhang99, BRENDA14]
L-arginine
12.0
[Lin88a, BRENDA14]
ATP
1200.0, 1900.0
[Gerlo82, BRENDA14]
ATP
2000.0
[Eriani90b, BRENDA14]
ATP
1350.0, 900.0
[Zhang99, BRENDA14]
ATP
900.0
[Lin88a, BRENDA14]
ATP
900.0
26.0
[Zhang98e, BRENDA14]

T(opt): 40 °C [Hirshfield69]

pH(opt) (forward direction): 8.1-8.5 [Charlier79]

pH(opt): 8.1 [BRENDA14, Charlier79]


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 122 -> 132
[UniProt10]
UniProt: "HIGH" region; Sequence Annotation Type: short sequence motif;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1876 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10071; confirmed by SwissProt match.


References

Airas06: Airas RK (2006). "Analysis of the kinetic mechanism of arginyl-tRNA synthetase." Biochim Biophys Acta 1764(2);307-19. PMID: 16427818

Airas96: Airas RK (1996). "Differences in the magnesium dependences of the class I and class II aminoacyl-tRNA synthetases from Escherichia coli." Eur J Biochem 240(1);223-31. PMID: 8797857

Aldinger12: Aldinger CA, Leisinger AK, Igloi GL (2012). "The influence of identity elements on the aminoacylation of tRNA(Arg) by plant and Escherichia coli arginyl-tRNA synthetases." FEBS J 279(19);3622-38. PMID: 22831759

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bi14a: Bi K, Zheng Y, Gao F, Dong J, Wang J, Wang Y, Gong W (2014). "Crystal structure of E. coli arginyl-tRNA synthetase and ligand binding studies revealed key residues in arginine recognition." Protein Cell 5(2);151-9. PMID: 24474195

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Chakraburtty80: Chakraburtty K (1980). "Recognition of E coli tRNAArg by arginyl tRNA synthetase." Nucleic Acids Res 8(19);4459-72. PMID: 6776488

Charlier76: Charlier J, Gerlo E (1976). "Arginyl-tRNA synthetase from Escherichia coli. Influence of arginine biosynthetic precursors on the charging of arginine-acceptor tRNA with [14C]arginine." Eur J Biochem 70(1);137-45. PMID: 795645

Charlier76a: Charlier J (1976). "On the behaviour of arginyl-tRNA synthetase of Escherichia coli in the presence of arginine precursors." Arch Int Physiol Biochim 84(3);588-90. PMID: 64171

Charlier79: Charlier J, Gerlo E (1979). "Arginyl-tRNA synthetase from Escherichia coli K12. Purification, properties, and sequence of substrate addition." Biochemistry 18(14);3171-8. PMID: 37899

Cheng91: Cheng XD, Lin SX, Shi JP, Wang YL (1991). "Arginyl-tRNA synthetase from Escherichia coli affinity labeling with 3'-oxidized tRNA(Arg)." Sci China B 34(3);297-305. PMID: 1708669

Cooper69a: Cooper PH, Hirshfield IN, Maas WK (1969). "Map location of arginyl-tRNA synthetase mutations in Escherichia coli K-12." Mol Gen Genet 104(4);383-90. PMID: 4904510

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Eriani89: Eriani G, Dirheimer G, Gangloff J (1989). "Isolation and characterization of the gene coding for Escherichia coli arginyl-tRNA synthetase." Nucleic Acids Res 17(14);5725-36. PMID: 2668891

Eriani90a: Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990). "Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs." Nature 347(6289);203-6. PMID: 2203971

Eriani90b: Eriani G, Dirheimer G, Gangloff J (1990). "Structure-function relationship of arginyl-tRNA synthetase from Escherichia coli: isolation and characterization of the argS mutation MA5002." Nucleic Acids Res 18(6);1475-9. PMID: 2183195

Faanes72: Faanes R, Rogers P (1972). "Repression of enzymes of arginine biosynthesis by L-canavanine in arginyl-transfer ribonucleic acid synthetase mutants of Escherichia coli." J Bacteriol 112(1);102-13. PMID: 4562386

Gerlo82: Gerlo E, Freist W, Charlier J (1982). "Arginyl-tRNA synthetase from Escherichia coli K12: specificity with regard to ATP analogs and their magnesium complexes." Hoppe Seylers Z Physiol Chem 363(4);365-73. PMID: 7042510

Giege12: Giege R, Springer M (2012). "Aminoacyl-tRNA Synthetases in the Bacterial World." EcoSal online, chapter 4.2.1.

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Godeau79: Godeau JM, Charlier J (1979). "Adenosine triphosphate consumption by bacterial arginyl-transfer ribonucleic acid synthetases." Biochem J 179(2);407-12. PMID: 384995

Gu96: Gu WL, Huang YW, Wang ED, Wang YL (1996). "The Spectroscopic Study of E. coli Arginyl-tRNA Synthetase (ArgRS) and its Mutants." Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 28(5);492-498. PMID: 12232610

Hirshfield68: Hirshfield IN, Horn PC, Hopwood DA, Maas WK, DeDeken R (1968). "Studies on the mechanism of repression of arginine biosynthesis in Escherichia coli. 3. Repression of enzymes of arginine biosynthesis in arginyl-tRNA synthetase mutants." J Mol Biol 35(1);83-93. PMID: 4939781

Hirshfield69: Hirshfield IN, Bloemers HP (1969). "The biochemical characterization of two mutant arginyl transfer ribonucleic acid synthetases from Escherichia coli K-12." J Biol Chem 244(11);2911-6. PMID: 4890761

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jakubowski95: Jakubowski H (1995). "Synthesis of cysteine-containing dipeptides by aminoacyl-tRNA synthetases." Nucleic Acids Res 23(22);4608-15. PMID: 8524650

Jovanovic99a: Jovanovic M, Lilic M, Janjusevic R, Jovanovic G, Savic DJ, Milija J (1999). "tRNA synthetase mutants of Escherichia coli K-12 are resistant to the gyrase inhibitor novobiocin." J Bacteriol 181(9);2979-83. PMID: 10217798

Kiga01: Kiga D, Sakamoto K, Sato S, Hirao I, Yokoyama S (2001). "Shifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase." Eur J Biochem 268(23);6207-13. PMID: 11733016

Kryzek76: Kryzek RA, Rogers P (1976). "Dual regulation by arginine of the expression of the Escherichia coli argECBH operon." J Bacteriol 126(1);348-64. PMID: 770426

Landes95: Landes C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL (1995). "A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases." Biochimie 77(3);194-203. PMID: 7647112

Lin88a: Lin SX, Shi JP, Cheng XD, Wang YL (1988). "Arginyl-tRNA synthetase from Escherichia coli, purification by affinity chromatography, properties, and steady-state kinetics." Biochemistry 27(17);6343-8. PMID: 3064807

Lin88b: Lin SX, Wang Q, Wang YL (1988). "Interactions between Escherichia coli arginyl-tRNA synthetase and its substrates." Biochemistry 27(17);6348-53. PMID: 3064808

Liu00: Liu MF, Li T, Yin ZB, Xu MG, Wang ED, Wang YL (2000). "A Strong Promoter Provided with the Gene Encoding Arginyl-tRNA Synthetase(argS) from Escherichia coli." Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 32(5);435-440. PMID: 12058187

Liu01: Liu MF, Xu MG, Xia X, Wang ED, Wang YL (2001). "A Negative Element Located in the Upstream Flanking Region of the Gene Encoding Arginyl-tRNA Synthetase (argS) from Escherichia coli." Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 33(6);621-628. PMID: 12035052

Liu02a: Liu W, Liu MF, Xia X, Wang ED, Wang YL (2002). "The effect of N-terminal changes on arginyl-tRNA synthetase from Escherichia coli." Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 34(2);131-7. PMID: 12007009

Liu99d: Liu M, Huang Y, Wu J, Wang E, Wang Y (1999). "Effect of cysteine residues on the activity of arginyl-tRNA synthetase from Escherichia coli." Biochemistry 38(34);11006-11. PMID: 10460155

Liu99e: Liu W, Wang ED, Wang YL (1999). "A Novel System for Hyper Expression and Rapid Purification of Arginyl-tRNA Synthetase from Escherichia coli." Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 31(5);494-498. PMID: 12114958

Lui78: Lui M, Chakraburtty K, Mehler AH (1978). "Partial reactions of aminoacyl-tRNA synthetases as functions of pH." J Biol Chem 253(22);8061-4. PMID: 30773

McClain90: McClain WH, Foss K, Jenkins RA, Schneider J (1990). "Nucleotides that determine Escherichia coli tRNA(Arg) and tRNA(Lys) acceptor identities revealed by analyses of mutant opal and amber suppressor tRNAs." Proc Natl Acad Sci U S A 87(23);9260-4. PMID: 2251270

Mehler67: Mehler AH, Mitra SK (1967). "The activation of arginyl transfer ribonucleic acid synthetase by transfer ribonucleic acid." J Biol Chem 242(23);5495-9. PMID: 12325365

Mitra67: Mitra SK, Mehler AH (1967). "The arginyl transfer ribonucleic acid synthetase of Escherichia coli." J Biol Chem 242(23);5490-4. PMID: 12325364

Neidhardt77: Neidhardt FC, Bloch PL, Pedersen S, Reeh S (1977). "Chemical measurement of steady-state levels of ten aminoacyl-transfer ribonucleic acid synthetases in Escherichia coli." J Bacteriol 129(1);378-87. PMID: 318645

Perona12: Perona JJ, Hadd A (2012). "Structural diversity and protein engineering of the aminoacyl-tRNA synthetases." Biochemistry 51(44);8705-29. PMID: 23075299

Reeh77: Reeh S, Pedersen S, Neidhardt FC (1977). "Transient rates of synthesis of five amionacyl-transfer ribonucleic acid synthetases during a shift-up of Escherichia coli." J Bacteriol 129(2);702-6. PMID: 320192

Schulman89: Schulman LH, Pelka H (1989). "The anticodon contains a major element of the identity of arginine transfer RNAs." Science 246(4937);1595-7. PMID: 2688091

Tamura92: Tamura K, Himeno H, Asahara H, Hasegawa T, Shimizu M (1992). "In vitro study of E.coli tRNA(Arg) and tRNA(Lys) identity elements." Nucleic Acids Res 20(9);2335-9. PMID: 1375736

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Vinella92: Vinella D, D'Ari R, Jaffe A, Bouloc P (1992). "Penicillin binding protein 2 is dispensable in Escherichia coli when ppGpp synthesis is induced." EMBO J 11(4);1493-501. PMID: 1563353

Wu98: Wu JF, Wang ED, Wang YL (1998). "Effect of Deletion of 245 and 252 Arginines in E. coli Arginyl-tRNA Synthetase on Its Structure and Function." Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 30(6);611-617. PMID: 12167998

Wu98a: Wu JF, Xia X, Wang ED, Wang YL (1998). "Study on the Overexpression of the Gene Encoding Arginyl-tRNA Synthetase under Induction." Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 30(3);236-240. PMID: 12174253

Yao03: Yao YN, Zhang QS, Yan XZ, Zhu G, Wang ED (2003). "Substrate-induced conformational changes in Escherichia coli arginyl-tRNA synthetase observed by 19F NMR spectroscopy." FEBS Lett 547(1-3);197-200. PMID: 12860413

Yao04: Yao YN, Zhang QS, Yan XZ, Zhu G, Wang ED (2004). "Escherichia coli tRNA(4)(Arg)(UCU) induces a constrained conformation of the crucial Omega-loop of arginyl-tRNA synthetase." Biochem Biophys Res Commun 313(1);129-34. PMID: 14672708

Yem71: Yem DW, Williams LS (1971). "Inhibition of arginyl-transfer ribonucleic acid synthetase activity of Escherichia coli by arginine biosynthetic precursors." J Bacteriol 107(2);589-91. PMID: 4939770

Zhang98e: Zhang QS, Wang ED, Wang YL (1998). "The role of tryptophan residues in Escherichia coli arginyl-tRNA synthetase." Biochim Biophys Acta 1387(1-2);136-42. PMID: 9748544

Zhang99: Zhang QS, Shen L, Wang ED, Wang YL (1999). "Biosynthesis and characterization of 4-fluorotryptophan-labeled Escherichia coli arginyl-tRNA synthetase." J Protein Chem 18(2);187-92. PMID: 10333292

Zhou07: Zhou M, Azzi A, Xia X, Wang ED, Lin SX (2007). "Crystallization and preliminary X-ray diffraction analysis of E. coli arginyl-tRNA synthetase in complex form with a tRNAArg." Amino Acids 32(4);479-82. PMID: 17061034

Zhou97a: Zhou M, Wang ED, Campbell RL, Wang YL, Lin SX (1997). "Crystallization and preliminary X-ray diffraction analysis of arginyl-tRNA synthetase from Escherichia coli." Protein Sci 6(12);2636-8. PMID: 9416614

Other References Related to Gene Regulation

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, BIOCYC13B.