Subsystem: Glutamate dehydrogenases

This subsystem's description is:

Interconversions of 2-ketoglutarate and glutamate are a major link between carbon and nitrogen metabolism in all living organisms. These reactions are catalyzed by several enzymes:

- glutamate dehydrogenase [2-ketoglutarate + NAD(P)H + NH3 + H+ ←→ L-glutamate + H2O +NAD(P)+],
- glutamate synthase [2-ketoglutarate + L-glutamine + NAD(P)H ←→ 2x glutamate +NAD(P)H],
- and glutamate aminotransferases [2-ketoglutarate + amino acid ←→ glutamate + keto acid]

This subsystem encodes only L-glutamate dehydrogenases (GDH). In general, GDHs fall into three classes based on their coenzyme specificity and their physiological function. NAD-dependent GDH (EC 1.4.1.2) is mainly involved in 2-oxoglutarate production (glutamate catabolism) and NADP-dependent GDH (EC 1.4.1.4) - in glutamate production (ammonia assimilation) in microorganisms. The GluDH that has dual coenzyme NAD(P)H specificity (EC 1.4.1.3) have been documented in the mammalian tissues, as well as in several microbial species, e.g. in Bacteroides fragilis (Abrahams et al., 1998), Sulfolobus solfataricus (Consalvi et al., 1991), and others.

An attempt was made in this SS to disambiguate L-glutamate dehydrogenases in regards to their cofactor specificity. GDH enzymes have been isolated and characterized in detail in a number of different microbial species – such proteins are associated with the corresponding references (as DLITs) in SEED. These annotations, as well as GDH annotations in closely related genomes are “locked”.
From these reference sequences cofactor specificity (NAD+, NADPH, or both) was projected to GDH proteins in taxonomically related organisms. However, the results of this attempted projection should be taken very cautiously, since large differences in NAD//NADP preference are often determined by changes in merely a few amino acid residues (e.g., Kujo et al., 1999)

In cases when cofactor specificity could not be reliably predicted from protein sequence, both functional annotation are associated with a protein (separated with a semicolon [;]) -
“NAD-specific glutamate dehydrogenase (EC 1.4.1.2) ; NADP-specific glutamate dehydrogenase (EC 1.4.1.4)”

On the other hand, the enzymes that have been experimentally shown to have dual cofactor NAD(P)H specificity are annotated here as “NAD-specific glutamate dehydrogenase (EC 1.4.1.2) / NADP-specific glutamate dehydrogenase (EC 1.4.1.4)” with a slash [/] (this annotation has replaced EC 1.4.1.3 referring to dual specificity)

References:

1. Majority of relevant publications are NOT listed here, but associated with the corresponding PEGs

2. Bhuiya MW, Sakuraba H, Kujo C, Nunoura-Kominato N, Kawarabayasi Y, Kikuchi H, Ohshima. Glutamate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1: enzymatic characterization, identification of the encoding gene, and phylogenetic implications. Extremophiles. 2000 Dec;4(6):333-41

3. Hashim S, Kwon DH, Abdelal A, Lu CD. The arginine regulatory protein mediates repression by arginine of the operons encoding glutamate synthase and anabolic glutamate dehydrogenase in Pseudomonas aeruginosa. J Bacteriol. 2004 Jun;186(12):3848-54

4. Kujo C., H. Sakuraba, N. Nunoura and T. Ohshima. The NAD-dependent glutamate dehydrogenase from the hyperthermophilic archaeon Pyrobaculum islandicum: cloning, sequencing, and expression of the enzyme gene. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology. Volume 1434, Issue 2, 12 October 1999, Pages 365-371

5. Lu CD, Abdelal AT. The gdhB gene of Pseudomonas aeruginosa encodes an arginine-inducible NAD(+)-dependent glutamate dehydrogenase which is subject to allosteric regulation. J Bacteriol. 2001 Jan;183(2):490-9

For more information, please check out the description and the additional notes tabs, below

DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional Notes 

Oops! We thought there was a diagram here, but we can't find it. Sorry

Group Alias
Abbrev.Functional RoleReactionsScenario ReactionsGOLiterature
SubsetsColoring
collapsed
expanded


  
display  items per page
«first  «prevdisplaying 1 - 2581 of 2581next»  last»
Taxonomy Pattern