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The N-Acetylglutamate Synthase Family: Structures, Function and Mechanisms.

Shi D, Allewell NM, Tuchman M - Int J Mol Sci (2015)

Bottom Line: Recent work has shown that several different genes encode enzymes that can catalyze NAG formation.Interestingly, these bifunctional enzymes have higher sequence similarity to vertebrate NAGS than those of the classical (mono-functional) bacterial NAGS.Solving the structures for both classical bacterial NAGS and bifunctional vertebrate-like NAGS/K has advanced our insight into the regulation and catalytic mechanisms of NAGS, and the evolutionary relationship between the two NAGS groups.

View Article: PubMed Central - PubMed

Affiliation: Center for Genetic Medicine Research and Department of Integrative Systems Biology, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA. dshi@childrensnational.org.

ABSTRACT
N-acetylglutamate synthase (NAGS) catalyzes the production of N-acetylglutamate (NAG) from acetyl-CoA and L-glutamate. In microorganisms and plants, the enzyme functions in the arginine biosynthetic pathway, while in mammals, its major role is to produce the essential co-factor of carbamoyl phosphate synthetase 1 (CPS1) in the urea cycle. Recent work has shown that several different genes encode enzymes that can catalyze NAG formation. A bifunctional enzyme was identified in certain bacteria, which catalyzes both NAGS and N-acetylglutamate kinase (NAGK) activities, the first two steps of the arginine biosynthetic pathway. Interestingly, these bifunctional enzymes have higher sequence similarity to vertebrate NAGS than those of the classical (mono-functional) bacterial NAGS. Solving the structures for both classical bacterial NAGS and bifunctional vertebrate-like NAGS/K has advanced our insight into the regulation and catalytic mechanisms of NAGS, and the evolutionary relationship between the two NAGS groups.

No MeSH data available.


Proposed evolutionary path of the bacteria-like and vertebrate-like NAGS. The domains that have and have not enzymatic activity are colored green and red, respectively. The genes for fungal NAGK and Haliangium ochraceum NAGS (marked with *) encode a three-domain preprotein, whose mature proteins are formed likely by cleaving the argC domain.
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ijms-16-13004-f006: Proposed evolutionary path of the bacteria-like and vertebrate-like NAGS. The domains that have and have not enzymatic activity are colored green and red, respectively. The genes for fungal NAGK and Haliangium ochraceum NAGS (marked with *) encode a three-domain preprotein, whose mature proteins are formed likely by cleaving the argC domain.

Mentions: Phylogenetic analysis has shown that classical bacteria and plant NAGS cluster in one group while bifunctional NAGS/K, fungal NAGK and NAGS, and vertebrate NAGS cluster in another large group [17]. The different quaternary structures of representative members of each group are consistent with the distant relationship between these two groups, implying that the separation of these two groups is a very early evolutionary event, as predicted previously [57]. However, the conservation of the arginine binding site and the general folding of the AAK domain indicate that the domains of both groups may be derived from the same common ancestor. The low sequence similarity and the non-conservation of the glutamate binding site in the NAT domains of the two groups demonstrate either that the NAT domains for different groups may come from different ancestors or that the separation of their NAT domains is likely a much earlier event before they fused with AAK domain to form NAGS. In the vertebrate-like NAGS group, the bifunctional NAGS/K appears to be the progenitor of other members positioned close to the root of the phylogenetic tree [17]. Interestingly, the bacteria whose genomes encode bifunctional NAGS/K also encode the gene for N-acetyl-l-ornithine transcarbamylase (AOTCase) in the arginine biosynthetic pathway, suggesting a coevolution of these two genes [17]. Phylogenetic analysis of the transcarbamylase family showed that the group of AOTCase clustering with N-succinyl-l-ornithine transcarbamylase [29] and YgeW encoded transcarbamylase of unknown function [58] is close to the root of the tree [59]. The primordial bifunctional NAGS/K evolved further to become the present day vertebrate NAGS, fungal NAGS and NAGK. The vertebrate NAGS and fungal NAGS preserved acetyltransferase activity, but lose the kinase activity while the fungal NAGK does the opposite. However, the present day fungal NAGK is formed by proteolytic processing of the biprotein precursor encoded by fusing an additional down-stream gene, argC [60,61]. Searches of the bacterial genomes reveal that the NAGS gene found in some bacteria appears to be the vestiges during this evolution. In the Azospirillum sp. B510 genome, the NAGS gene (AZL_c01370 is incorrectly annotated as argC, since argC encodes N-acetyl-γ-glutamyl-phosphate reductase), which has close sequence similarity with human (41.8%) and xcNAGS/K (76.7%), has lost its NAGK activity as a result of the elimination of key residues in the NAGK active site (R66D, N158G, K217T, E. coli NAGK numbering). Instead, a protein encoded by a different gene (AZL_005260) performs the NAGK function. In the Haliangium ochraceum genome, where there is a separate gene (Hoch_4935) for a bacterial-type NAGK, the gene for NAGS appears fused to the argC gene for N-acetyl-γ-glutamyl-phosphate reductase. Thus, this gene (Hoch_4300, incorrectly annotated as argC only) resembles the yeast gene encoding NAGK and N-acetyl-γ-glutamyl-phosphate reductase. Whether this protein in H. ochraceum undergoes proteolytic processing to cleave the argC domain as in yeast remains to be determined. The evolutionary paths of the typical NAGS are summarized in Figure 6.


The N-Acetylglutamate Synthase Family: Structures, Function and Mechanisms.

Shi D, Allewell NM, Tuchman M - Int J Mol Sci (2015)

Proposed evolutionary path of the bacteria-like and vertebrate-like NAGS. The domains that have and have not enzymatic activity are colored green and red, respectively. The genes for fungal NAGK and Haliangium ochraceum NAGS (marked with *) encode a three-domain preprotein, whose mature proteins are formed likely by cleaving the argC domain.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4490483&req=5

ijms-16-13004-f006: Proposed evolutionary path of the bacteria-like and vertebrate-like NAGS. The domains that have and have not enzymatic activity are colored green and red, respectively. The genes for fungal NAGK and Haliangium ochraceum NAGS (marked with *) encode a three-domain preprotein, whose mature proteins are formed likely by cleaving the argC domain.
Mentions: Phylogenetic analysis has shown that classical bacteria and plant NAGS cluster in one group while bifunctional NAGS/K, fungal NAGK and NAGS, and vertebrate NAGS cluster in another large group [17]. The different quaternary structures of representative members of each group are consistent with the distant relationship between these two groups, implying that the separation of these two groups is a very early evolutionary event, as predicted previously [57]. However, the conservation of the arginine binding site and the general folding of the AAK domain indicate that the domains of both groups may be derived from the same common ancestor. The low sequence similarity and the non-conservation of the glutamate binding site in the NAT domains of the two groups demonstrate either that the NAT domains for different groups may come from different ancestors or that the separation of their NAT domains is likely a much earlier event before they fused with AAK domain to form NAGS. In the vertebrate-like NAGS group, the bifunctional NAGS/K appears to be the progenitor of other members positioned close to the root of the phylogenetic tree [17]. Interestingly, the bacteria whose genomes encode bifunctional NAGS/K also encode the gene for N-acetyl-l-ornithine transcarbamylase (AOTCase) in the arginine biosynthetic pathway, suggesting a coevolution of these two genes [17]. Phylogenetic analysis of the transcarbamylase family showed that the group of AOTCase clustering with N-succinyl-l-ornithine transcarbamylase [29] and YgeW encoded transcarbamylase of unknown function [58] is close to the root of the tree [59]. The primordial bifunctional NAGS/K evolved further to become the present day vertebrate NAGS, fungal NAGS and NAGK. The vertebrate NAGS and fungal NAGS preserved acetyltransferase activity, but lose the kinase activity while the fungal NAGK does the opposite. However, the present day fungal NAGK is formed by proteolytic processing of the biprotein precursor encoded by fusing an additional down-stream gene, argC [60,61]. Searches of the bacterial genomes reveal that the NAGS gene found in some bacteria appears to be the vestiges during this evolution. In the Azospirillum sp. B510 genome, the NAGS gene (AZL_c01370 is incorrectly annotated as argC, since argC encodes N-acetyl-γ-glutamyl-phosphate reductase), which has close sequence similarity with human (41.8%) and xcNAGS/K (76.7%), has lost its NAGK activity as a result of the elimination of key residues in the NAGK active site (R66D, N158G, K217T, E. coli NAGK numbering). Instead, a protein encoded by a different gene (AZL_005260) performs the NAGK function. In the Haliangium ochraceum genome, where there is a separate gene (Hoch_4935) for a bacterial-type NAGK, the gene for NAGS appears fused to the argC gene for N-acetyl-γ-glutamyl-phosphate reductase. Thus, this gene (Hoch_4300, incorrectly annotated as argC only) resembles the yeast gene encoding NAGK and N-acetyl-γ-glutamyl-phosphate reductase. Whether this protein in H. ochraceum undergoes proteolytic processing to cleave the argC domain as in yeast remains to be determined. The evolutionary paths of the typical NAGS are summarized in Figure 6.

Bottom Line: Recent work has shown that several different genes encode enzymes that can catalyze NAG formation.Interestingly, these bifunctional enzymes have higher sequence similarity to vertebrate NAGS than those of the classical (mono-functional) bacterial NAGS.Solving the structures for both classical bacterial NAGS and bifunctional vertebrate-like NAGS/K has advanced our insight into the regulation and catalytic mechanisms of NAGS, and the evolutionary relationship between the two NAGS groups.

View Article: PubMed Central - PubMed

Affiliation: Center for Genetic Medicine Research and Department of Integrative Systems Biology, Children's National Medical Center, the George Washington University, Washington, DC 20010, USA. dshi@childrensnational.org.

ABSTRACT
N-acetylglutamate synthase (NAGS) catalyzes the production of N-acetylglutamate (NAG) from acetyl-CoA and L-glutamate. In microorganisms and plants, the enzyme functions in the arginine biosynthetic pathway, while in mammals, its major role is to produce the essential co-factor of carbamoyl phosphate synthetase 1 (CPS1) in the urea cycle. Recent work has shown that several different genes encode enzymes that can catalyze NAG formation. A bifunctional enzyme was identified in certain bacteria, which catalyzes both NAGS and N-acetylglutamate kinase (NAGK) activities, the first two steps of the arginine biosynthetic pathway. Interestingly, these bifunctional enzymes have higher sequence similarity to vertebrate NAGS than those of the classical (mono-functional) bacterial NAGS. Solving the structures for both classical bacterial NAGS and bifunctional vertebrate-like NAGS/K has advanced our insight into the regulation and catalytic mechanisms of NAGS, and the evolutionary relationship between the two NAGS groups.

No MeSH data available.