Escherichia coli K-12 substr. MG1655 Polypeptide: glutamate synthase, small subunit

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

Synonyms: psiQ, ossB, aspB

Regulation Summary Diagram

Regulation summary diagram for gltD

Component of:
glutamate synthase
glutamate synthase (extended summary available)

Gene Citations: [Castano88, Castano92, Grassl99, Paul07]

Locations: cytosol

Map Position: [3,357,220 -> 3,358,638] (72.36 centisomes, 260°)
Length: 1419 bp / 472 aa

Molecular Weight of Polypeptide: 52.015 kD (from nucleotide sequence), 53 kD (experimental) [Miller72 ]

pI: 7.4

Unification Links: ASAP:ABE-0010547, CGSC:17689, DIP:DIP-9803N, EchoBASE:EB0399, EcoGene:EG10404, EcoliWiki:b3213, Mint:MINT-1248739, ModBase:P09832, OU-Microarray:b3213, PortEco:gltD, PR:PRO_000022805, Pride:P09832, Protein Model Portal:P09832, RefSeq:NP_417680, RegulonDB:EG10404, SMR:P09832, String:511145.b3213, UniProt:P09832

Relationship Links: InterPro:IN-FAMILY:IPR001327, InterPro:IN-FAMILY:IPR006006, InterPro:IN-FAMILY:IPR009051, InterPro:IN-FAMILY:IPR016040, InterPro:IN-FAMILY:IPR017896, InterPro:IN-FAMILY:IPR028261, Pfam:IN-FAMILY:PF07992, Pfam:IN-FAMILY:PF13450, Pfam:IN-FAMILY:PF14691, Prosite:IN-FAMILY:PS51379

In Paralogous Gene Group: 381 (3 members)

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for gltD

GO Terms:
Biological Process:
Inferred from experimentInferred by computational analysisGO:0006537 - glutamate biosynthetic process [UniProtGOA11a, GOA01a, Miller72]
Inferred by computational analysisGO:0006807 - nitrogen compound metabolic process [UniProtGOA12]
Inferred by computational analysisGO:0008652 - cellular amino acid biosynthetic process [UniProtGOA11a]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0097054 - L-glutamate biosynthetic process [UniProtGOA12]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0004355 - glutamate synthase (NADPH) activity [GOA01, Miller72]
Inferred from experimentGO:0005515 - protein binding [Arifuzzaman06, Butland05]
Inferred by computational analysisGO:0004354 - glutamate dehydrogenase (NADP+) activity []
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016639 - oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor [GOA01a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08]
Inferred by computational analysisGO:0005737 - cytoplasm [Gaudet10]

MultiFun Terms: metabolismbiosynthesis of building blocksamino acidsglutamate
metabolismmetabolism of other compoundsnitrogen metabolism

Essentiality data for gltD knockouts:

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

Subunit of: glutamate synthase

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

Component of: glutamate synthase (extended summary available)

Subunit of: glutamate synthase


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

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: 800 kD (experimental) [Miller72]

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

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

Inferred from experiment

EC Number:

L-glutamine + 2-oxoglutarate + NADPH + H+ → 2 L-glutamate + NADP+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

In Pathways: L-glutamine degradation I, ammonia assimilation cycle III, L-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)

Inferred from experiment

EC Number:

L-glutamate + NADP+ + H2O ⇄ ammonium + 2-oxoglutarate + NADPH + H+

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

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]

Sequence Features

Protein sequence of glutamate synthase, small subunit with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Inferred from experiment[Wilkins98, Link97]
UniProt: Removed.
Chain 2 -> 472
Author statement[UniProt15]
UniProt: Glutamate synthase [NADPH] small chain.
Sequence-Conflict 38 -> 51
Inferred by curator[Oliver87, UniProt15]
UniProt: (in Ref. 1).
Conserved-Region 38 -> 69
Inferred by computational analysis[UniProt15]
UniProt: 4Fe-4S ferredoxin-type.
Metal-Binding-Site 94
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 98
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 104
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Metal-Binding-Site 108
Inferred by computational analysis[UniProt15]
UniProt: Iron-sulfur (4Fe-4S).
Sequence-Conflict 123
Inferred by curator[Oliver87, UniProt15]
UniProt: (in Ref. 1; AAA23905).
Sequence-Conflict 174
Inferred by curator[Oliver87, UniProt15]
UniProt: (in Ref. 1; AAA23905).
Sequence-Conflict 257 -> 270
Inferred by curator[Oliver87, UniProt15]
UniProt: (in Ref. 1).
Sequence-Conflict 312 -> 313
Inferred by curator[Oliver87, UniProt15]
UniProt: (in Ref. 1; AAA23905).
Sequence-Conflict 376 -> 400
Inferred by curator[Oliver87, UniProt15]
UniProt: (in Ref. 1; AAA23905).

Sequence Pfam Features

Protein sequence of glutamate synthase, small subunit with features indicated

Feature Class Location Citations Comment
Pfam PF14691 25 -> 134
Inferred by computational analysis[Finn14]
Fer4_20 : Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
Pfam PF13450 151 -> 185
Inferred by computational analysis[Finn14]
NAD_binding_8 : NAD(P)-binding Rossmann-like domain
Pfam PF07992 281 -> 459
Inferred by computational analysis[Finn14]
Pyr_redox_2 : Pyridine nucleotide-disulphide oxidoreductase

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


10/20/97 Gene b3213 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10404; confirmed by SwissProt match.


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

Castano88: Castano I, Bastarrachea F, Covarrubias AA (1988). "gltBDF operon of Escherichia coli." J Bacteriol 1988;170(2);821-7. PMID: 2448295

Castano92: Castano I, Flores N, Valle F, Covarrubias AA, Bolivar F (1992). "gltF, a member of the gltBDF operon of Escherichia coli, is involved in nitrogen-regulated gene expression." Mol Microbiol 1992;6(18);2733-41. PMID: 1447980

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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

Grassl99: Grassl G, Bufe B, Muller B, Rosel M, Kleiner D (1999). "Characterization of the gltF gene product of Escherichia coli." FEMS Microbiol Lett 1999;179(1);79-84. PMID: 10481090

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

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

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

Oliver87: Oliver G, Gosset G, Sanchez-Pescador R, Lozoya E, Ku LM, Flores N, Becerril B, Valle F, Bolivar F (1987). "Determination of the nucleotide sequence for the glutamate synthase structural genes of Escherichia coli K-12." Gene 60(1);1-11. PMID: 3326786

Paul07: Paul L, Mishra PK, Blumenthal RM, Matthews RG (2007). "Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgR." BMC Microbiol 7;2. PMID: 17233899

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

UniProtGOA11a: 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."

Wilkins98: Wilkins MR, Gasteiger E, Tonella L, Ou K, Tyler M, Sanchez JC, Gooley AA, Walsh BJ, Bairoch A, Appel RD, Williams KL, Hochstrasser DF (1998). "Protein identification with N and C-terminal sequence tags in proteome projects." J Mol Biol 278(3);599-608. PMID: 9600841

Other References Related to Gene Regulation

Calvo94: Calvo JM, Matthews RG (1994). "The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli." Microbiol Rev 58(3);466-90. PMID: 7968922

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Ernsting92: Ernsting BR, Atkinson MR, Ninfa AJ, Matthews RG (1992). "Characterization of the regulon controlled by the leucine-responsive regulatory protein in Escherichia coli." J Bacteriol 174(4);1109-18. PMID: 1346534

Ernsting93: Ernsting BR, Denninger JW, Blumenthal RM, Matthews RG (1993). "Regulation of the gltBDF operon of Escherichia coli: how is a leucine-insensitive operon regulated by the leucine-responsive regulatory protein?." J Bacteriol 175(22);7160-9. PMID: 7901196

Hommais04: Hommais F, Krin E, Coppee JY, Lacroix C, Yeramian E, Danchin A, Bertin P (2004). "GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli." Microbiology 150(Pt 1);61-72. PMID: 14702398

Krin10: Krin E, Danchin A, Soutourina O (2010). "Decrypting the H-NS-dependent regulatory cascade of acid stress resistance in Escherichia coli." BMC Microbiol 10;273. PMID: 21034467

Kumar11: Kumar R, Shimizu K (2011). "Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures." Microb Cell Fact 10;3. PMID: 21272324

Lintner08: Lintner RE, Mishra PK, Srivastava P, Martinez-Vaz BM, Khodursky AB, Blumenthal RM (2008). "Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio." BMC Microbiol 8;60. PMID: 18405378

Paul01: Paul L, Blumenthal RM, Matthews RG (2001). "Activation from a distance: roles of Lrp and integration host factor in transcriptional activation of gltBDF." J Bacteriol 183(13);3910-8. PMID: 11395454

Velazquez91: Velazquez L, Camarena L, Reyes JL, Bastarrachea F (1991). "Mutations affecting the Shine-Dalgarno sequences of the untranslated region of the Escherichia coli gltBDF operon." J Bacteriol 173(10);3261-4. PMID: 1673677

Wiese97: Wiese DE, Ernsting BR, Blumenthal RM, Matthews RG (1997). "A nucleoprotein activation complex between the leucine-responsive regulatory protein and DNA upstream of the gltBDF operon in Escherichia coli." J Mol Biol 270(2);152-68. PMID: 9236118

Zimmer00: Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S (2000). "Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation." Proc Natl Acad Sci U S A 97(26);14674-9. PMID: 11121068

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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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