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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.


Arginine binding site and conformational changes. (A) Ribbon diagram of subunit structure of ngNAGS in the presence of arginine; (B) Ribbon diagram of subunit structure of mmNAGS/K in the presence of arginine. Arginine is shown in space filling model; (C) The details of arginine binding site of ngNAGS; (D) The details of arginine binding site of mmNAGS/K. The arginine and key residues involved in binding arginine are shown in sticks; (E) Simplified model of quaternary structure in the presence of arginine; and (F) The K3-S1 interface of ngNAGS in the presence of arginine.
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ijms-16-13004-f005: Arginine binding site and conformational changes. (A) Ribbon diagram of subunit structure of ngNAGS in the presence of arginine; (B) Ribbon diagram of subunit structure of mmNAGS/K in the presence of arginine. Arginine is shown in space filling model; (C) The details of arginine binding site of ngNAGS; (D) The details of arginine binding site of mmNAGS/K. The arginine and key residues involved in binding arginine are shown in sticks; (E) Simplified model of quaternary structure in the presence of arginine; and (F) The K3-S1 interface of ngNAGS in the presence of arginine.

Mentions: Structural and mutagenesis studies show that the arginine-binding site of NAGS and arginine sensitive NAGK is conserved across phyla [42,46,47,56]. The arginine-binding site is located at the C-terminus of the AAK domain, close to the AAK and NAT domain interface and the C-terminal segment of the N-terminal helix of protein (helix 1 in ngNAGS, helix 2 in mmNAGS/K) (Figure 5A,B). The primary sequence has a conserved motif of E-(L/I)-(F/M)-(T/S)-X-X-G-X-G-T [56], which forms a loop connecting the last helix and the last β strand of the AAK domain. The arginine binds to the protein in such a way as to place the Cα on the N-terminal helix, the α-carboxyl group towards the central β-sheet and the side-chain to be encircled by the loop. A key lysine from the central β-sheet (K201 in ngNAGS and K206 in mmNAGS/K) and a key glutamate from the last helix of AAK domain (E270 in ngNAGS and E277 in mmNAGS/K) with many main-chain oxygen atoms help to position arginine in this position (Figure 5C,D).


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

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

Arginine binding site and conformational changes. (A) Ribbon diagram of subunit structure of ngNAGS in the presence of arginine; (B) Ribbon diagram of subunit structure of mmNAGS/K in the presence of arginine. Arginine is shown in space filling model; (C) The details of arginine binding site of ngNAGS; (D) The details of arginine binding site of mmNAGS/K. The arginine and key residues involved in binding arginine are shown in sticks; (E) Simplified model of quaternary structure in the presence of arginine; and (F) The K3-S1 interface of ngNAGS in the presence of arginine.
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Related In: Results  -  Collection

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ijms-16-13004-f005: Arginine binding site and conformational changes. (A) Ribbon diagram of subunit structure of ngNAGS in the presence of arginine; (B) Ribbon diagram of subunit structure of mmNAGS/K in the presence of arginine. Arginine is shown in space filling model; (C) The details of arginine binding site of ngNAGS; (D) The details of arginine binding site of mmNAGS/K. The arginine and key residues involved in binding arginine are shown in sticks; (E) Simplified model of quaternary structure in the presence of arginine; and (F) The K3-S1 interface of ngNAGS in the presence of arginine.
Mentions: Structural and mutagenesis studies show that the arginine-binding site of NAGS and arginine sensitive NAGK is conserved across phyla [42,46,47,56]. The arginine-binding site is located at the C-terminus of the AAK domain, close to the AAK and NAT domain interface and the C-terminal segment of the N-terminal helix of protein (helix 1 in ngNAGS, helix 2 in mmNAGS/K) (Figure 5A,B). The primary sequence has a conserved motif of E-(L/I)-(F/M)-(T/S)-X-X-G-X-G-T [56], which forms a loop connecting the last helix and the last β strand of the AAK domain. The arginine binds to the protein in such a way as to place the Cα on the N-terminal helix, the α-carboxyl group towards the central β-sheet and the side-chain to be encircled by the loop. A key lysine from the central β-sheet (K201 in ngNAGS and K206 in mmNAGS/K) and a key glutamate from the last helix of AAK domain (E270 in ngNAGS and E277 in mmNAGS/K) with many main-chain oxygen atoms help to position arginine in this position (Figure 5C,D).

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.