d -Ala– d -X ligases: evaluation of d -alanyl phosphate intermediate by MIX, PIX and rapid quench studies

Healy, Vicki L; Mullins, Leisha S.; Li, Xianfeng; Hall, Steven E.; Raushel, Frank M.; Walsh, Christopher T.

doi:10.1016/s1074-5521(00)00135-6

Cited by 24 publications

(15 citation statements)

References 43 publications

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“…A number of poly(amino acids) such as folyl‐poly γ‐glutamate play roles in the housekeeping functions of their producer cells and like the muramyl peptide chains, the tripeptide glutathione or the d ‐Ala‐ d ‐Ala dipeptides of the bacterial cell walls are formed by amino‐acid ligases such as UDP‐ N ‐acetyl‐muramoyl‐ l ‐alanine‐glutamate ligase, glutathione synthetase or d ‐Ala‐ d ‐Ala ligase [37]. They condense carboxylate‐containing compounds via the intermediacy of acylphosphates as in the case of formation of the d ‐Ala‐ d ‐Ala dipeptide [38]. Remarkably, in several compounds synthesized by this mechanism, unusual peptide bonds sych as the γ‐glutamyl peptide bond also occur as in the muramyl peptides and glutathione.…”

Section: Discussionmentioning

confidence: 99%

A β‐lysine adenylating enzyme and a β‐lysine binding protein involved in poly β‐lysine chain assembly in nourseothricin synthesis in Streptomyces noursei

Grammel

Pankevych

Demydchuk

et al. 2002

European Journal of Biochemistry

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Nourseothricins (syn. Streptothricins), a group of nucleoside peptides produced by several streptomycete strains, contain a poly b-lysine chain of variable length attached in amide linkage to the amino sugar moiety gulosamine of the nucleoside portion. We show that the nourseothricin-producing Streptomyces noursei contains an enzyme (NpsA) of an apparent M r 56 000 that speci®cally activates b-lysine by adenylation but does not bind to it as a thioester. Cloning and sequencing of npsA from S. noursei including its¯ank-ing DNA regions revealed that it is closely linked to the nourseothricin resistance gene nat1 and some other genes on the chromosome possibly involved in nourseothricin biosynthesis. The deduced amino-acid sequence revealed that NpsA is a stand-alone adenylation domain with similarity to the adenylation domains of nonribosomal peptide synthetases (NRPS). Further analysis revealed that S. noursei contains a b-lysine binding enzyme (NpsB) of about M r 64 100 which can be loaded by NpsA with b-lysine as a thioester. Analysis of the deduced amino-acid sequence from the gene (npsB) of NpsB showed that it consists of two domains. The N-terminal domain of 100 amino-acid residues has high similarity to PCP domains of NRPSs whereas the 450-amino-acid C-terminal domain has a high similarity to epimerization (E)-domains of NRPSs. Remarkably, in this E-domain the conserved H-H-motif is changed to H-Q, which suggests that either the domain is nonfunctional or has a specialized function. The presence of one single adenylating b-lysine activating enzyme in nourseothricin-producing streptomycete and a separate binding protein suggests an iteratively operating NRPS-module catalyses synthesis of the poly b-lysine chain.

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Section: Discussionmentioning

confidence: 99%

A β‐lysine adenylating enzyme and a β‐lysine binding protein involved in poly β‐lysine chain assembly in nourseothricin synthesis in Streptomyces noursei

Grammel

Pankevych

Demydchuk

et al. 2002

European Journal of Biochemistry

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“…Evidence for the formation of this intermediate has been determined from positional isotope exchange studies which have shown that a labeled oxygen atom from the carboxylic acid is transferred to the inorganic phosphate product (Figure 5). [47-53] The existence of the acylphosphate intermediate is also supported by diazomethane trapping studies on carbamoyl phosphate synthetase which trapped the reactive intermediate, carboxyphosphate. [54] Formation of an acylphosphate intermediate has been implicated by the discovery of highly potent mechanistic inhibitors of DDLigase which mimic the reaction of a nucleophile with this phosphorylated intermediate (see the section 6 for additional details).…”

Section: Mechanismmentioning

confidence: 99%

The ATP-grasp enzymes

Fawaz

Topper

Firestine

2011

Bioorganic Chemistry

163

178

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The ATP-grasp enzymes consist of a superfamily of 21 proteins that contain an atypical ATP-binding site, called the ATP-grasp fold. The ATP-grasp fold is comprised of two α + β domains that “grasp” a molecule of ATP between them and members of the family typically have an overall structural design containing 3 common conserved focal domains. The founding members of the family consist of biotin carboxylase, D-ala-D-ala ligase and glutathione synthetase, all of which catalyze the ATP-assisted reaction of a carboxylic acid with a nucleophile via the formation of an acylphosphate intermediate. While most members of the superfamily follow this mechanistic pathway, studies have demonstrated that two enzymes catalyze only the phosphoryl transfer step and thus are kinases instead of ligases. Members of the ATP-grasp superfamily are found in several metabolic pathways including de novo purine biosynthesis, gluconeogenesis and fatty acid synthesis. Given the critical nature of these enzymes, researchers have actively sought the development of potent inhibitors of several members of the superfamily as antibacterial and anti-obseity agents. In this review, we will discuss the structure, function, mechanism and inhibition of the ATP-grasp enzymes.

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“…The reaction starts with the attack on the first D-Ala by the g-phosphate of ATP, to give an acylphosphate. This is followed by an attack by the amino group of the second D-Ala to yield a tetrahedral intermediate, which collapses into D-Ala-D-Ala and P i (Mullins et al, 1990;Healy et al, 2000b). In this respect, the mechanism is similar to that of the Mur ligases (see 'Biosynthesis of the UDP-MurNAcpeptides').…”

Section: Formation Of D-ala -D-alamentioning

confidence: 99%

Cytoplasmic steps of peptidoglycan biosynthesis

et al. 2008

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The biosynthesis of bacterial cell wall peptidoglycan is a complex process that involves enzyme reactions that take place in the cytoplasm (synthesis of the nucleotide precursors) and on the inner side (synthesis of lipid-linked intermediates) and outer side (polymerization reactions) of the cytoplasmic membrane. This review deals with the cytoplasmic steps of peptidoglycan biosynthesis, which can be divided into four sets of reactions that lead to the syntheses of (1) UDP-N-acetylglucosamine from fructose 6-phosphate, (2) UDP-N-acetylmuramic acid from UDP-N-acetylglucosamine, (3) UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid and (4) D-glutamic acid and dipeptide D-alanyl-D-alanine. Recent data concerning the different enzymes involved are presented. Moreover, special attention is given to (1) the chemical and enzymatic synthesis of the nucleotide precursor substrates that are not commercially available and (2) the search for specific inhibitors that could act as antibacterial compounds.

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d -Ala– d -X ligases: evaluation of d -alanyl phosphate intermediate by MIX, PIX and rapid quench studies

Abstract: These three approaches support the rapid (more than 1000 min(-1)), reversible formation of the enzyme intermediate D-Ala(1)-P by members of the D-Ala-D-X (where X is Ala, Ser or Lac) ligase superfamily.

Cited by 24 publications

References 43 publications

A β‐lysine adenylating enzyme and a β‐lysine binding protein involved in poly β‐lysine chain assembly in nourseothricin synthesis in Streptomyces noursei

A β‐lysine adenylating enzyme and a β‐lysine binding protein involved in poly β‐lysine chain assembly in nourseothricin synthesis in Streptomyces noursei

The ATP-grasp enzymes

Cytoplasmic steps of peptidoglycan biosynthesis

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