Application | Comment | Organism |
---|---|---|
drug development | although AtGDH1 is insensitive to MPD in activity assays, several (+/-)-2-methyl-2,4-pentanediol (MPD) binding sites with conserved sequence are identified and the observation of druggable sites opens a potential for non-competitive herbicide design | Arabidopsis thaliana |
Crystallization (Comment) | Organism |
---|---|
purified recombinant AtGDH1 in the apo-form and in complex with NAD+, X-ray diffraction structure determination and analysis at 2.59 and 2.03 A resolution, respectively. Most of the subunits in the crystal structures, including those in NAD+ complex, are in open conformation, with domain II forming a large (albeit variable) angle with domain I. One of the subunits of the AtGDH1-NAD+ hexamer contains a serendipitous 2-oxoglutarate molecule in the active site, causing a dramatic closure of the domains | Arabidopsis thaliana |
structure of recombinant GDH1 in the apo-form and in complex with NAD+ at 2.59 and 2.03 A resolution, respectively. Both in the apo form and in 1:1 complex with NAD+, it forms D3-symmetric homohexamers. A subunit of GDH1 consists of domain I, which is involved in hexamer formation and substrate binding, and of domain II which binds coenzyme | Arabidopsis thaliana |
Inhibitors | Comment | Organism | Structure |
---|---|---|---|
2-methyl-2,4-pentanediol | 8.5 mM, 94% residual activity. the sequence contains several binding sites for 2-methyl-2,4-pentanediol | Arabidopsis thaliana | |
Ca2+ | 0.1 mM, 82% residual activity; 8% inhibition at 0.1 mM, 23% at 1 mM | Arabidopsis thaliana | |
Co2+ | 0.1 mM, 77% residual activity; 23% inhibition at 0.1 mM | Arabidopsis thaliana | |
Cu2+ | 0.1 mM, 65% residual activity; 35% inhibition at 0.1 mM | Arabidopsis thaliana | |
additional information | not inhibitory: Mn2+ | Arabidopsis thaliana | |
Zn2+ | 0.1 mM, 51% residual activity; 49% inhibition at 0.1 mM | Arabidopsis thaliana |
KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
2.5 | 5 | L-glutamate | pH 7.5, 25°C | Arabidopsis thaliana | |
2.5 | 5 | L-glutamate | with NAD+, recombinant enzyme, pH and temperature not specified in the publication | Arabidopsis thaliana |
Localization | Comment | Organism | GeneOntology No. | Textmining |
---|---|---|---|---|
mitochondrion | the N-terminal peptide preceding domain I is a mitochondrial targeting signal, the predicted cleavage site is Leu17-Leu18 followed by an potassium coordination site (Ser27, Ile30) | Arabidopsis thaliana | 5739 | - |
mitochondrion | the N-terminal peptide preceding domain I is a mitochondrial targeting signal, with a predicted cleavage site for mitochondrial processing peptidase (MPP) at Leu17-Leu18 that is followed by an unexpected potassium coordination site (Ser27, Ile30) | Arabidopsis thaliana | 5739 | - |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
additional information | GDH1 shows no sensitivity to Mn2+ | Arabidopsis thaliana |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
L-glutamate + H2O + NAD+ | Arabidopsis thaliana | AtGDH1 activity in the forward reaction (oxidative deamination) is physiologically more relevant due to the high NAD+/NADH ratio in plant mitochondria | 2-oxoglutarate + NH3 + NADH + H+ | - |
r |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Arabidopsis thaliana | Q43314 | - |
- |
Posttranslational Modification | Comment | Organism |
---|---|---|
proteolytic modification | the N-terminal peptide preceding domain I is a mitochondrial targeting signal, the predicted cleavage site is Leu17-Leu18 followed by an potassium coordination site (Ser27, Ile30) | Arabidopsis thaliana |
proteolytic modification | the N-terminal peptide preceding domain I is a mitochondrial targeting signal, with a predicted cleavage site for mitochondrial processing peptidase (MPP) at Leu17-Leu18 that is followed by an unexpected potassium coordination site (Ser27, Ile30) | Arabidopsis thaliana |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
L-glutamate + H2O + NAD+ | - |
Arabidopsis thaliana | 2-oxoglutarate + NH3 + NADH + H+ | - |
? | |
L-glutamate + H2O + NAD+ | - |
Arabidopsis thaliana | 2-oxoglutarate + NH3 + NADH + H+ | - |
r | |
L-glutamate + H2O + NAD+ | AtGDH1 activity in the forward reaction (oxidative deamination) is physiologically more relevant due to the high NAD+/NADH ratio in plant mitochondria | Arabidopsis thaliana | 2-oxoglutarate + NH3 + NADH + H+ | - |
r |
Subunits | Comment | Organism |
---|---|---|
homohexamer | both in the apo form and in 1:1 complex with NAD+, it forms D3-symmetric homohexamers, composed of alpha-subunits | Arabidopsis thaliana |
More | one subunit of AtGDH1 consists of domain I, which is involved in hexamer formation and substrate binding, and domain II, which binds the coenzyme. Most of the subunits in the crystal structures, including those in NAD+ complex, are in open conformation, with domain II forming a large (albeit variable) angle with domain I. One of the subunits of the AtGDH1-NAD+ hexamer contains a serendipitous 2-oxoglutarate molecule in the active site, causing a dramatic closure of the domains | Arabidopsis thaliana |
Synonyms | Comment | Organism |
---|---|---|
At5g18170 | locus name | Arabidopsis thaliana |
AtGDH1 | - |
Arabidopsis thaliana |
GDH1 | - |
Arabidopsis thaliana |
glutamate dehydrogenase isoform 1 | - |
Arabidopsis thaliana |
type I GDH | - |
Arabidopsis thaliana |
Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
13.3 | - |
L-glutamate | pH 7.5, 25°C | Arabidopsis thaliana | |
13.3 | - |
L-glutamate | with NAD+, recombinant enzyme, pH and temperature not specified in the publication | Arabidopsis thaliana |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
additional information | no detectable activity with NADP+ | Arabidopsis thaliana | |
additional information | AtGDH1 in the presence of NADP+ instead of NAD+ shows no activity. Dynamics of the coafctor binding domain II, cofactor binding mode, overview | Arabidopsis thaliana | |
NAD+ | - |
Arabidopsis thaliana | |
NAD+ | one NAD+ binds molecule per AtGDH1 subunit, Kd value 0.072 mM | Arabidopsis thaliana | |
NADH | - |
Arabidopsis thaliana |
General Information | Comment | Organism |
---|---|---|
evolution | GDHs are members of a superfamily of ELFV (Glu/Leu/Phe/Val) amino acid dehydrogenases and are subdivided into three subclasses, based on coenzyme specificity: NAD+-specific, NAD+/NADP+ dual-specific, and NADP+-specific. The mitochondrial AtGDH1 isozyme from Arabidopsis thaliana is NAD+-specific. Arabidopsis thaliana expresses three GDH isozymes (AtGDH1-3) targeted to mitochondria, of which AtGDH2 has an extra EF-hand motif and is stimulated by calcium, while AtGDH1's sensitivity to calcium is negligible. In vivo the AtGDH1-3 enzymes form homo- and heterohexamers of varied composition. Phylogenetic analysis of GDHs in plants. Plants have distinct isozymes of GDH that are either NAD or NADP-specific. NAD-specific GDHs are localized in mitochondria, whereas NADP-specific GDHs exist in chloroplasts. The sequence region 257-264 in AtGDH1 and AtGDH2, which directly precedes the EF-hand motif in AtGDH2 (residues 265-277), is the most altered region of AtGDH2 in comparison with AtGDH1 | Arabidopsis thaliana |
metabolism | GDH contributes to Glu homeostasis and plays a significant role at the junction of carbon and nitrogen assimilation pathways | Arabidopsis thaliana |
additional information | several (+/-)-2-methyl-2,4-pentanediol (MPD) binding sites with conserved sequence are identified, but AtGDH1 is insensitive to MPD in activity assays. Structure function analysis of AtGDH1, overview. The open-to-closed conformational transition is required to form a fully functional active site | Arabidopsis thaliana |
physiological function | glutamate dehydrogenase (GDH) releases ammonia in a reversible NAD(P)+-dependent oxidative deamination of glutamate that yields 2-oxoglutarate (2OG). Plants have distinct isozymes of GDH that are either NAD or NADP-specific. NAD-specific GDHs are localized in mitochondria, whereas NADP-specific GDHs exist in chloroplasts | Arabidopsis thaliana |
kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
5.22 | - |
L-glutamate | with NAD+, recombinant enzyme, pH and temperature not specified in the publication | Arabidopsis thaliana |