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Escherichia coli K-12 substr. MG1655 Enzyme: glutamate synthase

Synonyms: NADPH-GOGAT

Subunit composition of glutamate synthase = [(GltD)(GltB)]4
         glutamate synthase = (GltD)(GltB)
                 glutamate synthase, small subunit = GltD
                 glutamate synthase, large subunit = GltB

Summary:
Glutamate synthase catalyzes the single-step conversion of L-glutamine and alpha-ketoglutarate into two molecules of L-glutamate. In doing so, it simultaneously operates as the major source of L-glutamate for the cell and as a key step in ammonia assimilation during nitrogen-limited growth.

Glutamate synthase catalyzes the production of L-glutamate from L-glutamine and alpha-ketoglutarate [Miller72, Berberich72, Lozoya80]. In addition to L-glutamine, glutamate synthase can also use ammonia as a nitrogen source for the generation of L-glutamate from alpha-ketoglutarate. The ammonia-dependent reaction does not require flavin or iron like the L-glutamine-dependent reaction, but is also much slower than that reaction, with about 5-7% of its activity [Mantsala76]. Both the L-glutamine- and ammonia-dependent reactions are reversible, at about 10% of the rate of the forward reaction [Mantsala76, Mantsala76a]. Despite this similarity, the two reactions appear to occur by different mechanisms. In the L-glutamine-dependent reaction, the NADPH reduces the enzyme itself, most likely at the flavin cofactor, and then the enzyme is oxidized again during the reaction of L-glutamine and alpha-ketoglutarate to yield two L-glutamates. In this mode, hydrogen from NADPH ends up as a component of water. In the ammonia-dependent reaction, the enzyme is neither reduced nor oxidized, and hydrogen from NADPH ends up in the single L-glutamate that is produced from alpha-ketoglutarate [Mantsala76b, Mantsala76a, Miller72, Geary77].

Glutamate synthase is a tetramer of dimers, with each dimer having one large and one small subunit (GltB and GltD, respectively) [Miller72]. The ammonia-dependent activity can be catalyzed very slowly by just the small subunit in the absence of the full complex [Mantsala76]. Ligand-binding interactions with glutamate synthase have been examined [Bower83].

The gltBDF operon that codes for both components of glutamate synthase is induced by phosphate starvation [Metcalf90]. Glutamate synthase abundance is also inversely proportional to the percent of charged tRNA-Glu present in the cell, and can experience up to a 10-fold increase in mutants with temporarily diminished glutamyl-tRNA synthetase function [Lapointe75].

Mutants lacking glutamate synthase function grow poorly on all nitrogen sources other than ammonia due to a critical lack of glutamate [Goss01]. Glutamate synthase mutants are also osmosensitive, even in an ammonia-rich environment [Saroja96].

Molecular Weight of Multimer: 800 kD (experimental) [Miller72]

Gene-Reaction Schematic: ?

Credits:
Last-Curated ? 16-Feb-2012 by Shearer A , SRI International


Enzymatic reaction of: L-glutamate:NADP+ oxidoreductase (transaminating) (glutamate synthase)

EC Number: 1.4.1.13

L-glutamine + 2-oxoglutarate + NADPH + H+ <=> 2 L-glutamate + NADP+

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.

In Pathways: glutamine degradation I , ammonia assimilation cycle III , glutamate biosynthesis I

Cofactors or Prosthetic Groups: FAD [Geary77, Miller72], Fe2+ [Miller72]

Inhibitors (Unknown Mechanism): D-aspartate [Miller72] , L-aspartate [Miller72] , D-glutamate [Miller72] , L-methionine [Miller72]

Kinetic Parameters:

Substrate
Km (μM)
Citations
L-glutamine
250.0
[Miller72]

pH(opt): 7.6 [Miller72]


Enzymatic reaction of: L-glutamate:NADP+ oxidoreductase (deaminating) (glutamate synthase)

EC Number: 1.4.1.4

L-glutamate + NADP+ + H2O <=> ammonium + 2-oxoglutarate + NADPH + H+

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

This reaction is reversible.

Summary:
This reaction is reversible [Mantsala76a]. The pH optimum for the reverse reaction is 9.4 [Mantsala76a].

Kinetic Parameters:

Substrate
Km (μM)
Citations
2-oxoglutarate
240.0
[Mantsala76a]
NADPH
14.0
[Mantsala76a]

pH(opt): 8.4 [Mantsala76a]


Subunit of glutamate synthase: glutamate synthase, small subunit

Synonyms: OssB, PsiQ, AspB, GltD

Gene: gltD Accession Numbers: EG10404 (EcoCyc), b3213, ECK3203

Locations: cytosol

Sequence Length: 472 AAs

Molecular Weight: 52.015 kD (from nucleotide sequence)

Molecular Weight: 53 kD (experimental) [Miller72]

pI: 7.4

GO Terms:

Biological Process: GO:0006537 - glutamate biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01a, Miller72]
GO:0006807 - nitrogen compound metabolic process Inferred by computational analysis [UniProtGOA12]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0097054 - L-glutamate biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0004355 - glutamate synthase (NADPH) activity Inferred from experiment Inferred by computational analysis [GOA01, Miller72]
GO:0005515 - protein binding Inferred from experiment [Arifuzzaman06, Butland05]
GO:0004354 - glutamate dehydrogenase (NADP+) activity Inferred by computational analysis
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0016639 - oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0050660 - flavin adenine dinucleotide binding Inferred by computational analysis [GOA01a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids glutamate
metabolism metabolism of other compounds nitrogen metabolism

Unification Links: DIP:DIP-9803N , EcoliWiki:b3213 , Mint:MINT-1248739 , ModBase:P09832 , PR:PRO_000022805 , Pride:P09832 , Protein Model Portal:P09832 , RefSeq:NP_417680 , SMR:P09832 , String:511145.b3213 , UniProt:P09832

Relationship Links: InterPro:IN-FAMILY:IPR001327 , InterPro:IN-FAMILY:IPR006006 , InterPro:IN-FAMILY:IPR009051 , InterPro:IN-FAMILY:IPR012285 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR017896 , InterPro:IN-FAMILY:IPR028261 , Pfam:IN-FAMILY:PF00070 , Pfam:IN-FAMILY:PF14691 , Prosite:IN-FAMILY:PS51379

Essentiality data for gltD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Subunit of glutamate synthase: glutamate synthase, large subunit

Synonyms: OssB, PsiQ, AspB, GltB

Gene: gltB Accession Numbers: EG10403 (EcoCyc), b3212, ECK3202

Locations: cytosol

Sequence Length: 1517 AAs

Molecular Weight: 166.71 kD (from nucleotide sequence)

Molecular Weight: 135 kD (experimental) [Miller72]

GO Terms:

Biological Process: GO:0006537 - glutamate biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01a, Miller72]
GO:0006541 - glutamine metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0006807 - nitrogen compound metabolic process Inferred by computational analysis [UniProtGOA12, GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0097054 - L-glutamate biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0004355 - glutamate synthase (NADPH) activity Inferred from experiment Inferred by computational analysis [GOA01, Miller72]
GO:0005515 - protein binding Inferred from experiment [Arifuzzaman06, Butland05]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0004354 - glutamate dehydrogenase (NADP+) activity Inferred by computational analysis
GO:0015930 - glutamate synthase activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0016638 - oxidoreductase activity, acting on the CH-NH2 group of donors Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
GO:0051538 - 3 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Ishihama08]

MultiFun Terms: metabolism biosynthesis of building blocks amino acids glutamate
metabolism metabolism of other compounds nitrogen metabolism

Unification Links: DIP:DIP-9802N , EcoliWiki:b3212 , Mint:MINT-1248755 , ModBase:P09831 , PR:PRO_000022804 , Pride:P09831 , Protein Model Portal:P09831 , RefSeq:NP_417679 , SMR:P09831 , String:511145.b3212 , UniProt:P09831

Relationship Links: InterPro:IN-FAMILY:IPR000583 , InterPro:IN-FAMILY:IPR002489 , InterPro:IN-FAMILY:IPR002932 , InterPro:IN-FAMILY:IPR006982 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR017932 , Pfam:IN-FAMILY:PF00310 , Pfam:IN-FAMILY:PF01493 , Pfam:IN-FAMILY:PF01645 , Pfam:IN-FAMILY:PF04898 , Prosite:IN-FAMILY:PS51278

Essentiality data for gltB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

References

Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

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

Berberich72: Berberich MA (1972). "A glutamate-dependent phenotype in E. coli K12: the result of two mutations." Biochem Biophys Res Commun 47(6);1498-503. PMID: 4402696

Bower83: Bower S, Zalkin H (1983). "Chemical modification and ligand binding studies with Escherichia coli glutamate synthase." Biochemistry 22(7);1613-20. PMID: 6342664

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Geary77: Geary LE, Meister A (1977). "On the mechanism of glutamine-dependent reductive amination of alpha-ketoglutarate catalyzed by glutamate synthase." J Biol Chem 1977;252(10);3501-8. PMID: 16906

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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."

Goss01: Goss TJ, Perez-Matos A, Bender RA (2001). "Roles of glutamate synthase, gltBD, and gltF in nitrogen metabolism of Escherichia coli and Klebsiella aerogenes." J Bacteriol 183(22);6607-19. PMID: 11673431

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

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lapointe75: Lapointe J, Delcuve G, Duplain L (1975). "Derepressed levels of glutamate synthase and glutamine synthetase in Escherichia coli mutants altered in glutamyl-transfer ribonucleic acid synthetase." J Bacteriol 123(3);843-50. PMID: 239924

Lozoya80: Lozoya E, Sanchez-Pescador R, Covarrubias A, Vichido I, Bolivar F (1980). "Tight linkage of genes that encode the two glutamate synthase subunits of Escherichia coli K-12." J Bacteriol 144(2);616-21. PMID: 6107287

Mantsala76: Mantsala P, Zalkin H (1976). "Active subunits of Escherichia coli glutamate synthase." J Bacteriol 1976;126(1);539-41. PMID: 770440

Mantsala76a: Mantsala P, Zalkin H (1976). "Properties of apoglutamate synthase and comparison with glutamate dehydrogenase." J Biol Chem 251(11);3300-5. PMID: 6450

Mantsala76b: Mantsala P, Zalkin H (1976). "Glutamate synthase. Properties of the glutamine-dependent activity." J Biol Chem 251(11);3294-9. PMID: 6449

Metcalf90: Metcalf WW, Steed PM, Wanner BL (1990). "Identification of phosphate starvation-inducible genes in Escherichia coli K-12 by DNA sequence analysis of psi::lacZ(Mu d1) transcriptional fusions." J Bacteriol 172(6);3191-200. PMID: 2160940

Miller72: Miller RE, Stadtman ER (1972). "Glutamate synthase from Escherichia coli. An iron-sulfide flavoprotein." J Biol Chem 247(22);7407-19. PMID: 4565085

Saroja96: Saroja GN, Gowrishankar J (1996). "Roles of SpoT and FNR in NH4+ assimilation and osmoregulation in GOGAT (glutamate synthase)-deficient mutants of Escherichia coli." J Bacteriol 178(14);4105-14. PMID: 8763938

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."


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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, biocyc13.