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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.


Related in: MedlinePlus

Ribbon diagram of subunit structures of ngNAGS and mmNAGS/K. (A) Subunit structure of ngNAGS in the absence of arginine. The structure consists of two domains, amino acid kinase (AAK) domain and N-acetyltransferase (NAT) domain, linked together by a flexible linker. No domain-domain interactions are observed within the subunit except via the linker; (B) Subunit structure of mmNAGS/K in the absence of arginine. The linker between AAK and NAT domains is shorter than that in ngNAGS. Some domain-domain interactions are observed. The structures are colored as a rainbow gradually changed from dark-blue for the N-terminus to red for the C-terminus; (C) Ribbon diagram of the NAT domain of ngNAGS. The bound CoA and NAG are shown in green and magenta sticks, respectively. Three residues, R416, R425 and S427, which are involved in binding NAG, are shown as green sticks; and (D) Ribbon diagram of NAT domain of mmNAGS/K. The last helix, α15, occupies the equivalent position of α14 of ngNAGS. Three residues, R386, R388 and N391, which are potentially involved in binding NAG, are shown as green sticks. The major differences in the NAT domains between ngNAGS and mmNAGS/K are colored in red.
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ijms-16-13004-f002: Ribbon diagram of subunit structures of ngNAGS and mmNAGS/K. (A) Subunit structure of ngNAGS in the absence of arginine. The structure consists of two domains, amino acid kinase (AAK) domain and N-acetyltransferase (NAT) domain, linked together by a flexible linker. No domain-domain interactions are observed within the subunit except via the linker; (B) Subunit structure of mmNAGS/K in the absence of arginine. The linker between AAK and NAT domains is shorter than that in ngNAGS. Some domain-domain interactions are observed. The structures are colored as a rainbow gradually changed from dark-blue for the N-terminus to red for the C-terminus; (C) Ribbon diagram of the NAT domain of ngNAGS. The bound CoA and NAG are shown in green and magenta sticks, respectively. Three residues, R416, R425 and S427, which are involved in binding NAG, are shown as green sticks; and (D) Ribbon diagram of NAT domain of mmNAGS/K. The last helix, α15, occupies the equivalent position of α14 of ngNAGS. Three residues, R386, R388 and N391, which are potentially involved in binding NAG, are shown as green sticks. The major differences in the NAT domains between ngNAGS and mmNAGS/K are colored in red.

Mentions: Determination of the crystal structures of NAGS from Neisseria gonorrhoeae (ngNAGS), which belongs to the classical bacteria-like NAGS group, and bifunctional NAGS/K structures from Maricaulis maris (mmNAGS/K) and Xanthomonas campestrics (xcNAGS/K), which belong to the vertebrate-like NAGS group including mammalian NAGS allows detailed structural characterization of each group possible. Even though there are significant sequence differences between the bacteria-like and vertebrate-like groups, both consist of two independent domains [44,45] (Figure 2A,B). Furthermore, the overall fold of each domain of these two groups of NAGS is very similar, although some differences exist. The N-terminal domain has typical the AAK domain with an eight-stranded β sheet as its central core and α helices hanging on both sides. The superimposition of AAK domains of mmNAGS and ngNAGS results in a root mean square deviation of 2.7 Å, with over 260 aligned residues. The most significant differences are identified in the N-terminal segment. The N-terminal segment of mmNAGS/K has two helices; in contrast, ngNAGS has only one as does arginine sensitive NAGK while arginine insensitive NAGK has no mobile N-terminal helix. The differences in their N-terminal segments appear to be highly correlated to their different subunit-subunit interactions and formation of different quaternary structures. The C-terminal has typical GNAT fold with a seven-stranded β sheet as its central core and three α helices hanging on both sides to form αβα sandwich structure. Superimposition of the NAT domain of mmNAGS/K and ngNAGS results in a root mean square deviation of 2.5 Å, with 112 aligned residues. Significant differences are found in the C-terminal arm. mNAGS/K has a much shorter loop to link β18 and β19 than ngNAGS, which has two extra helices (α14’ and α14) (Figure 2C). Instead, a long helix, α15, at the C-terminal of mmNAGS/K occupies the equivalent position of α14 in ngNAGS (Figure 2D). A 1–3 amino acid residue flexible linker fuses the two domains. The relative orientation between the two domains appears to be affected by inhibitor binding and the different packing environments in crystal structures, and appears to be closely related to the regulation mechanism [44,46,47].


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

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

Ribbon diagram of subunit structures of ngNAGS and mmNAGS/K. (A) Subunit structure of ngNAGS in the absence of arginine. The structure consists of two domains, amino acid kinase (AAK) domain and N-acetyltransferase (NAT) domain, linked together by a flexible linker. No domain-domain interactions are observed within the subunit except via the linker; (B) Subunit structure of mmNAGS/K in the absence of arginine. The linker between AAK and NAT domains is shorter than that in ngNAGS. Some domain-domain interactions are observed. The structures are colored as a rainbow gradually changed from dark-blue for the N-terminus to red for the C-terminus; (C) Ribbon diagram of the NAT domain of ngNAGS. The bound CoA and NAG are shown in green and magenta sticks, respectively. Three residues, R416, R425 and S427, which are involved in binding NAG, are shown as green sticks; and (D) Ribbon diagram of NAT domain of mmNAGS/K. The last helix, α15, occupies the equivalent position of α14 of ngNAGS. Three residues, R386, R388 and N391, which are potentially involved in binding NAG, are shown as green sticks. The major differences in the NAT domains between ngNAGS and mmNAGS/K are colored in red.
© Copyright Policy
Related In: Results  -  Collection

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

ijms-16-13004-f002: Ribbon diagram of subunit structures of ngNAGS and mmNAGS/K. (A) Subunit structure of ngNAGS in the absence of arginine. The structure consists of two domains, amino acid kinase (AAK) domain and N-acetyltransferase (NAT) domain, linked together by a flexible linker. No domain-domain interactions are observed within the subunit except via the linker; (B) Subunit structure of mmNAGS/K in the absence of arginine. The linker between AAK and NAT domains is shorter than that in ngNAGS. Some domain-domain interactions are observed. The structures are colored as a rainbow gradually changed from dark-blue for the N-terminus to red for the C-terminus; (C) Ribbon diagram of the NAT domain of ngNAGS. The bound CoA and NAG are shown in green and magenta sticks, respectively. Three residues, R416, R425 and S427, which are involved in binding NAG, are shown as green sticks; and (D) Ribbon diagram of NAT domain of mmNAGS/K. The last helix, α15, occupies the equivalent position of α14 of ngNAGS. Three residues, R386, R388 and N391, which are potentially involved in binding NAG, are shown as green sticks. The major differences in the NAT domains between ngNAGS and mmNAGS/K are colored in red.
Mentions: Determination of the crystal structures of NAGS from Neisseria gonorrhoeae (ngNAGS), which belongs to the classical bacteria-like NAGS group, and bifunctional NAGS/K structures from Maricaulis maris (mmNAGS/K) and Xanthomonas campestrics (xcNAGS/K), which belong to the vertebrate-like NAGS group including mammalian NAGS allows detailed structural characterization of each group possible. Even though there are significant sequence differences between the bacteria-like and vertebrate-like groups, both consist of two independent domains [44,45] (Figure 2A,B). Furthermore, the overall fold of each domain of these two groups of NAGS is very similar, although some differences exist. The N-terminal domain has typical the AAK domain with an eight-stranded β sheet as its central core and α helices hanging on both sides. The superimposition of AAK domains of mmNAGS and ngNAGS results in a root mean square deviation of 2.7 Å, with over 260 aligned residues. The most significant differences are identified in the N-terminal segment. The N-terminal segment of mmNAGS/K has two helices; in contrast, ngNAGS has only one as does arginine sensitive NAGK while arginine insensitive NAGK has no mobile N-terminal helix. The differences in their N-terminal segments appear to be highly correlated to their different subunit-subunit interactions and formation of different quaternary structures. The C-terminal has typical GNAT fold with a seven-stranded β sheet as its central core and three α helices hanging on both sides to form αβα sandwich structure. Superimposition of the NAT domain of mmNAGS/K and ngNAGS results in a root mean square deviation of 2.5 Å, with 112 aligned residues. Significant differences are found in the C-terminal arm. mNAGS/K has a much shorter loop to link β18 and β19 than ngNAGS, which has two extra helices (α14’ and α14) (Figure 2C). Instead, a long helix, α15, at the C-terminal of mmNAGS/K occupies the equivalent position of α14 in ngNAGS (Figure 2D). A 1–3 amino acid residue flexible linker fuses the two domains. The relative orientation between the two domains appears to be affected by inhibitor binding and the different packing environments in crystal structures, and appears to be closely related to the regulation mechanism [44,46,47].

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.


Related in: MedlinePlus