Hydroxamate-based colorimetric assay to assess amide bond formation by adenylation domain of nonribosomal peptide synthetases

2015 ◽  
Vol 477 ◽  
pp. 89-91 ◽  
Author(s):  
Ryotaro Hara ◽  
Ryohei Suzuki ◽  
Kuniki Kino
Keyword(s):  
Colorimetric Assay ◽  
Bond Formation ◽  
Amide Bond ◽  
Adenylation Domain ◽  
Nonribosomal Peptide ◽  
Nonribosomal Peptide Synthetases ◽  
Peptide Synthetases ◽  
Amide Bond Formation

scholarly journals Structural and mutational analysis of the nonribosomal peptide synthetase heterocyclization domain provides insight into catalysis

2016 ◽  
Vol 114 (1) ◽  
pp. 95-100 ◽  
Author(s):  
Kristjan Bloudoff ◽  
Christopher D. Fage ◽  
Mohamed A. Marahiel ◽  
T. Martin Schmeing
Keyword(s):  
Peptide Synthesis ◽  
Active Sites ◽  
Mutational Analysis ◽  
Bond Formation ◽  
Amide Bond ◽  
Active Site Residues ◽  
Nonribosomal Peptide ◽  
Amide Bond Formation ◽  
Catalytic Mechanisms ◽  
Insight Into

Nonribosomal peptide synthetases (NRPSs) are a family of multidomain, multimodule enzymes that synthesize structurally and functionally diverse peptides, many of which are of great therapeutic or commercial value. The central chemical step of peptide synthesis is amide bond formation, which is typically catalyzed by the condensation (C) domain. In many NRPS modules, the C domain is replaced by the heterocyclization (Cy) domain, a homologous domain that performs two consecutive reactions by using hitherto unknown catalytic mechanisms. It first catalyzes amide bond formation, and then the intramolecular cyclodehydration between a Cys, Ser, or Thr side chain and the backbone carbonyl carbon to form a thiazoline, oxazoline, or methyloxazoline ring. The rings are important for the form and function of the peptide product. We present the crystal structure of an NRPS Cy domain, Cy2 of bacillamide synthetase, at a resolution of 2.3 Å. Despite sharing the same fold, the active sites of C and Cy domains have important differences. The structure allowed us to probe the roles of active-site residues by using mutational analyses in a peptide synthesis assay with intact bacillamide synthetase. The drastically different effects of these mutants, interpreted by using our structural and bioinformatic results, provide insight into the catalytic mechanisms of the Cy domain and implicate a previously unexamined Asp-Thr dyad in catalysis of the cyclodehydration reaction.

scholarly journals Exploring the Adenylation Domain Repertoire of Nonribosomal Peptide Synthetases Using an Ensemble of Sequence-Search Methods

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e65926 ◽  
Author(s):  
Guillermin Agüero-Chapin ◽  
Reinaldo Molina-Ruiz ◽  
Emanuel Maldonado ◽  
Gustavo de la Riva ◽  
Aminael Sánchez-Rodríguez ◽  
...  
Keyword(s):  
Adenylation Domain ◽  
Search Methods ◽  
Nonribosomal Peptide ◽  
Nonribosomal Peptide Synthetases ◽  
Peptide Synthetases ◽  
Sequence Search

Diethylphosphoryl-OxymaB (DEPO-B) as a Solid Coupling Reagent for Amide Bond Formation

2018 ◽  
Vol 16 (1) ◽  
pp. 30-33
Author(s):  
Ashish Kumar ◽  
Yahya E. Jad ◽  
Ayman El-Faham ◽  
Beatriz G. de la Torre ◽  
Fernando Albericio
Keyword(s):  
Bond Formation ◽  
Hydrolytic Stability ◽  
Solid Material ◽  
Amide Bond ◽  
Amide Bond Formation ◽  
Coupling Reagent

A new phosphonium based coupling reagent DEPO-B has been synthesized from 5- (hydroxyimino)-1,3-dimethylpyrimidine-2,4,6 (1H,3H,5H)-trione (Oxyma B) and diethyl chlorophosphate in presence of base. It is a solid material and the hydrolytic stability and solubility was evaluated for confirming its capability for usage in automated peptide synthesizer.

A Review of Amide Bond Formation in Microwave Organic Synthesis

2014 ◽  
Vol 11 (4) ◽  
pp. 592-604 ◽  
Author(s):  
Natalia Lukasik ◽  
Ewa Wagner-Wysiecka
Keyword(s):  
Organic Synthesis ◽  
Bond Formation ◽  
Amide Bond ◽  
Amide Bond Formation

A computational study on the mechanism of ynamide-mediated amide bond formation from carboxylic acids and amines

2017 ◽  
Vol 15 (30) ◽  
pp. 6367-6374 ◽  
Author(s):  
Song-Lin Zhang ◽  
Hai-Xing Wan ◽  
Zhu-Qin Deng
Keyword(s):  
Reaction Mechanism ◽  
Carboxylic Acids ◽  
Computational Study ◽  
Bond Formation ◽  
Amide Bond ◽  
Reactivity Pattern ◽  
Amide Bond Formation ◽  
Coupling Reagent ◽  
Catalytic Effects ◽  
Acid Substrate

A detailed computational study is presented on the reaction mechanism of ynamide-mediated condensation of carboxylic acids with amines to produce amides, which elucidates the reactivity pattern of the coupling reagent ynamide and discloses crucial bifunctional catalytic effects of the carboxylic acid substrate during aminolysis.

Green Amide Bond Formation in Water via Direct Coupling of Metal Carboxylate Salts with Ammonium Salts at Room Temperature

2021 ◽  
Author(s):  
Truong Thanh Tung ◽  
John Nielsen
Keyword(s):  
Room Temperature ◽  
Bond Formation ◽  
Direct Coupling ◽  
Ammonium Salts ◽  
Amide Bond ◽  
Metal Carboxylate ◽  
Amide Bond Formation ◽  
Simple Protocol

Herein, we report the green, expedite, and practically simple protocol for direct coupling of carboxylate salts and ammonium salts under ACN/H2O conditions at room temperature without the addition of tertiary...

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