Escherichia coli K-12 substr. MG1655 Polypeptide: glycyl-tRNA synthetase, β subunit

Gene: glyS Accession Numbers: EG10410 (EcoCyc), b3559, ECK3547

Synonyms: glyS(B), gly, gly-act

Regulation Summary Diagram: ?

Regulation summary diagram for glyS

Component of: glycyl-tRNA synthetase (summary available)

A β subunit cysteine thiol is not required for catalytic activity; however, C395 can be alkylated by NEM, resulting in loss of GlyRS activity [Profy86]. The N-terminal domain of the β subunit contains residues required for adenylate synthesis, while the C-terminal domain appears to be dispensable for catalytic activity [Toth90].

The isolated β subunit binds tRNAGly; there is one binding site per monomer [Nagel84].

Gene Citations: [Webster83]

Locations: cytosol

Map Position: [3,720,351 <- 3,722,420] (80.19 centisomes, 289°)
Length: 2070 bp / 689 aa

Molecular Weight of Polypeptide: 76.813 kD (from nucleotide sequence), 65 kD (experimental) [Keng82 ]

Unification Links: ASAP:ABE-0011624 , CGSC:674 , DIP:DIP-6880N , EchoBASE:EB0405 , EcoGene:EG10410 , EcoliWiki:b3559 , Mint:MINT-1276197 , OU-Microarray:b3559 , PortEco:glyS , PR:PRO_000022818 , Pride:P00961 , Protein Model Portal:P00961 , RefSeq:NP_418016 , RegulonDB:EG10410 , String:511145.b3559 , UniProt:P00961

Relationship Links: InterPro:IN-FAMILY:IPR006194 , InterPro:IN-FAMILY:IPR008909 , InterPro:IN-FAMILY:IPR015944 , Pfam:IN-FAMILY:PF02092 , Pfam:IN-FAMILY:PF05746 , Prints:IN-FAMILY:PR01045 , Prosite:IN-FAMILY:PS50861 , Smart:IN-FAMILY:SM00836

In Paralogous Gene Group: 449 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [UniProtGOA11a]
GO:0006420 - arginyl-tRNA aminoacylation Inferred by computational analysis [GOA01a]
GO:0006426 - glycyl-tRNA aminoacylation Inferred by computational analysis [GOA06, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Hauser14, Rajagopala14]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [UniProtGOA11a]
GO:0004814 - arginine-tRNA ligase activity Inferred by computational analysis [GOA01a]
GO:0004820 - glycine-tRNA ligase activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: information transfer protein related amino acid -activation

Essentiality data for glyS knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

Subunit of: glycyl-tRNA synthetase

Subunit composition of glycyl-tRNA synthetase = [GlyS]2[GlyQ]2
         glycyl-tRNA synthetase, β subunit = GlyS (summary available)
         glycyl-tRNA synthetase, α subunit = GlyQ

Glycyl-tRNA synthetase (GlyRS) 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. GlyRS belongs to the Class II aminoacyl tRNA synthetases, which share three regions of homology [Eriani90, Cusack91].

GlyRS is a tetramer consisting of two α and two β subunits. Both subunits are required for catalytic activity [Ostrem70, McDonald80]. An enzyme in which the α and β subunits are fused into a single polypeptide chain is catalytically active [Toth86].

Specificity determinants within tRNAGly that are important for recognition by GlyRS have been identified [Roberts75, McClain91, Hipps95, Nameki97]. The tRNA binding site is located in the β subunit of GlyRS [Nagel84].

Review: [Ibba00]

Molecular Weight: 205 kD (experimental) [McDonald80]

Last-Curated ? 20-Jun-2006 by Keseler I , SRI International

Enzymatic reaction of: glycyl-tRNA synthetase

Synonyms: GlyRS

EC Number:

a tRNAgly + glycine + ATP + H+ <=> a glycyl-[tRNAgly] + AMP + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA charging

Kinetic Parameters:

Km (μM)
14.0, 40.0, 42.0
[Ostrem74, BRENDA14]
30.0, 140.0, 160.0
[Ostrem74, BRENDA14]
a tRNAgly
[Ostrem74, BRENDA14]
a tRNAgly
0.68, 2.1
[Nameki97, BRENDA14]

Sequence Features

Protein sequence of glycyl-tRNA synthetase, beta subunit with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Link97, UniProt11a]
UniProt: Removed.
Sequence-Conflict 2
[Webster83, UniProt10]
UniProt: (in Ref. 1; AAA23915);
Chain 2 -> 689
UniProt: Glycyl-tRNA synthetase beta subunit;
Sequence-Conflict 91
[Webster83, UniProt10]
UniProt: (in Ref. 1; AAA23915);
Sequence-Conflict 154 -> 156
[Webster83, UniProt10]
UniProt: (in Ref. 1; AAA23915);
Sequence-Conflict 211 -> 212
[Webster83, UniProt10]
UniProt: (in Ref. 1; AAA23915);
Sequence-Conflict 342
[Webster83, UniProt10]
UniProt: (in Ref. 1; AAA23915);
Sequence-Conflict 361
[Webster83, UniProt10]
UniProt: (in Ref. 1; AAA23915);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3559 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10410; confirmed by SwissProt match.


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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Cusack91: Cusack S, Hartlein M, Leberman R (1991). "Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases." Nucleic Acids Res 19(13);3489-98. PMID: 1852601

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

Eriani90: 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

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."

Hauser14: Hauser R, Ceol A, Rajagopala SV, Mosca R, Siszler G, Wermke N, Sikorski P, Schwarz F, Schick M, Wuchty S, Aloy P, Uetz P (2014). "A Second-generation Protein-Protein Interaction Network of Helicobacter pylori." Mol Cell Proteomics 13(5);1318-29. PMID: 24627523

Hipps95: Hipps D, Schimmel P (1995). "Cell growth inhibition by sequence-specific RNA minihelices." EMBO J 14(16);4050-5. PMID: 7664744

Ibba00: Ibba M, Soll D (2000). "Aminoacyl-tRNA synthesis." Annu Rev Biochem 69;617-50. PMID: 10966471

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

Keng82: Keng T, Webster TA, Sauer RT, Schimmel P (1982). "Gene for Escherichia coli glycyl-tRNA synthetase has tandem subunit coding regions in the same reading frame." J Biol Chem 257(21);12503-8. PMID: 6290471

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

McClain91: McClain WH, Foss K, Jenkins RA, Schneider J (1991). "Rapid determination of nucleotides that define tRNA(Gly) acceptor identity." Proc Natl Acad Sci U S A 88(14);6147-51. PMID: 2068095

McDonald80: McDonald T, Breite L, Pangburn KL, Hom S, Manser J, Nagel GM (1980). "Overproduction, purification, and subunit structure of Escherichia coli glycyl transfer ribonucleic acid synthetase." Biochemistry 19(7);1402-9. PMID: 6992865

Nagel84: Nagel GM, Cumberledge S, Johnson MS, Petrella E, Weber BH (1984). "The beta subunit of E. coli glycyl-tRNA synthetase plays a major role in tRNA recognition." Nucleic Acids Res 12(10);4377-84. PMID: 6374618

Nameki97: Nameki N, Tamura K, Asahara H, Hasegawa T (1997). "Recognition of tRNA(Gly) by three widely diverged glycyl-tRNA synthetases." J Mol Biol 268(3);640-7. PMID: 9171287

Ostrem70: Ostrem DL, Berg P (1970). "Glycyl-tRNA synthetase: an oligomeric protein containing dissimilar subunits." Proc Natl Acad Sci U S A 67(4);1967-74. PMID: 4923123

Ostrem74: Ostrem DL, Berg P (1974). "Glycyl transfer ribonucleic acid synthetase from Escherichia coli: purification, properties, and substrate binding." Biochemistry 13(7);1338-48. PMID: 4594761

Profy86: Profy AT, Schimmel P (1986). "A sulfhydryl presumed essential is not required for catalysis by an aminoacyl-tRNA synthetase." J Biol Chem 261(33);15474-9. PMID: 3536904

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Roberts75: Roberts JW, Carbon J (1975). "Nucleotide sequence studies of normal and genetically altered glycine transfer ribonucleic acids from Escherichia coli." J Biol Chem 250(14);5530-41. PMID: 167016

Toth86: Toth MJ, Schimmel P (1986). "Internal structural features of E. coli glycyl-tRNA synthetase examined by subunit polypeptide chain fusions." J Biol Chem 261(15);6643-6. PMID: 3009467

Toth90: Toth MJ, Schimmel P (1990). "Deletions in the large (beta) subunit of a hetero-oligomeric aminoacyl-tRNA synthetase." J Biol Chem 265(2);1000-4. PMID: 2404005

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

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

Webster83: Webster TA, Gibson BW, Keng T, Biemann K, Schimmel P (1983). "Primary structures of both subunits of Escherichia coli glycyl-tRNA synthetase." J Biol Chem 258(17);10637-41. PMID: 6309809

Yamamoto09: Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H (2009). "Update on the Keio collection of Escherichia coli single-gene deletion mutants." Mol Syst Biol 5;335. PMID: 20029369

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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