The role of LasR active site amino acids in the interaction with the Acyl Homoserine Lactones (AHLs) analogues: A computational study

2019 ◽  
Vol 86 ◽  
pp. 113-124 ◽  
Author(s):  
Maicol Ahumedo Monterrosa ◽  
Johan Fabian Galindo ◽  
Javier Vergara Lorduy ◽  
Jorge Alí-Torres ◽  
Ricardo Vivas-Reyes
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
Computational Study ◽  
Homoserine Lactones ◽  
Acyl Homoserine Lactones

Peroxovanadates and Its Bio-Mimicking Relation with Vanadium Haloperoxidases

2016 ◽  
pp. 197-219
Author(s):  
Pranjal Saikia ◽  
Saitanya Kumar Bharadwaj ◽  
Abu Taleb Miah
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
High Efficiency ◽  
Recombinant Enzymes ◽  
Vanadium Compounds ◽  
Reaction Conditions ◽  
The Cost ◽  
Major Emphasis ◽  
Protein Active Site

Vanadium Haloperoxidases (VHPOs) have been used in a variety of biotransformations showing remarkable stereoselectivity and regiospecificity. The high efficiency of the enzyme is influenced by the protein active site and the role of certain amino acids in activation of vanadium(V)-bound peroxide for halide oxidation. The use of natural or recombinant enzymes, or biomimetic vanadium compounds brings up issues regarding the cost of production and reaction conditions. In this chapter, the primary intent is to provide a simple and clear picture of functional mimicking nature of peroxovanadium compounds with haloperoxidases enzymes to the readers. Major emphasis would be given to examine the reactivity of the vanadium haloperoxidases with mechanism.

scholarly journals The mechanism of action of dd-peptidases: the role of Threonine-299 and -301 in the Streptomyces R61 dd-peptidase

1994 ◽  
Vol 301 (2) ◽  
pp. 477-483 ◽  
Author(s):  
J M Wilkin ◽  
A Dubus ◽  
B Joris ◽  
J M Frère
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Peptide Substrate ◽  
Binding Properties ◽  
Beta Lactamases ◽  
Penicillin Binding Proteins ◽  
Active Site Cavity

The side chains of residues Thr299 and Thr301 in the Streptomyces R61 DD-peptidase have been modified by site-directed mutagenesis. These amino acids are part of a beta-strand which forms a wall of the active-site cavity. Thr299 corresponds to the second residue of the Lys-Thr(Ser)-Gly triad, highly conserved in active-site beta-lactamases and penicillin-binding proteins (PBPs). Modification of Thr301 resulted only in minor alterations of the catalytic and penicillin-binding properties of the enzyme. No selective decrease of the rate of acylation was observed for any particular class of compounds. By contrast, the loss of the hydroxy group of the residue in position 299 yielded a seriously impaired enzyme. The rates of inactivation by penicillins were decreased 30-50-fold, whereas the reactions with cephalosporins were even more affected. The efficiency of hydrolysis against the peptide substrate was also seriously decreased. More surprisingly, the mutant was completely unable to catalyse transpeptidation reactions. The conservation of an hydroxylated residue in this position in PBPs is thus easily explained by these results.

The role of N-acyl homoserine lactones in maintaining the stability of aerobic granules

2014 ◽  
Vol 159 ◽  
pp. 305-310 ◽  
Author(s):  
Yaochen Li ◽  
Wen Hao ◽  
Junping Lv ◽  
Yaqin Wang ◽  
Chen Zhong ◽  
...  
Keyword(s):  
Aerobic Granules ◽  
Homoserine Lactones ◽  
Acyl Homoserine Lactones ◽  
The Stability

scholarly journals Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Komal Ishwar Pawar ◽  
Katta Suma ◽  
Ayshwarya Seenivasan ◽  
Santosh Kumar Kuncha ◽  
Satya Brata Routh ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Active Site ◽  
Unknown Function ◽  
Physiological Importance ◽  
Cellular Defense

Strict L-chiral rejection through Gly-cisPro motif during chiral proofreading underlies the inability of D-aminoacyl-tRNA deacylase (DTD) to discriminate between D-amino acids and achiral glycine. The consequent Gly-tRNAGly ‘misediting paradox’ is resolved by EF-Tu in the cell. Here, we show that DTD’s active site architecture can efficiently edit mischarged Gly-tRNAAla species four orders of magnitude more efficiently than even AlaRS, the only ubiquitous cellular checkpoint known for clearing the error. Also, DTD knockout in AlaRS editing-defective background causes pronounced toxicity in Escherichia coli even at low-glycine levels which is alleviated by alanine supplementation. We further demonstrate that DTD positively selects the universally invariant tRNAAla-specific G3•U70. Moreover, DTD’s activity on non-cognate Gly-tRNAAla is conserved across all bacteria and eukaryotes, suggesting DTD’s key cellular role as a glycine deacylator. Our study thus reveals a hitherto unknown function of DTD in cracking the universal mechanistic dilemma encountered by AlaRS, and its physiological importance.

scholarly journals Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen

Biomolecules ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1679
Author(s):  
Olivier Nicolas Lemaire ◽  
Marie-Caroline Müller ◽  
Jörg Kahnt ◽  
Tristan Wagner
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
Methanogenic Archaea ◽  
Branched Chain Amino Acids ◽  
Structural Rearrangements ◽  
Coenzyme Binding ◽  
High Conservation ◽  
Branched Chain ◽  
Very High

Ketol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to understand their remarkable specificity towards NADH or NADPH, but also to develop antibiotics. Here, we present the first structural study on a KARI natively isolated from a methanogenic archaea. The dodecameric structure of 0.44-MDa was obtained in two different conformations, an open and close state refined to a resolution of 2.2-Å and 2.1-Å, respectively. These structures illustrate the conformational movement required for substrate and coenzyme binding. While the close state presents the complete NADP bound in front of a partially occupied Mg2+-site, the Mg2+-free open state contains a tartrate at the nicotinamide location and a bound NADP with the adenine-nicotinamide protruding out of the active site. Structural comparisons show a very high conservation of the active site environment and detailed analyses point towards few specific residues required for the dodecamerisation. These residues are not conserved in other dodecameric KARIs that stabilise their trimeric interface differently, suggesting that dodecamerisation, the cellular role of which is still unknown, might have occurred several times in the evolution of KARIs.

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