Helicobacter pylori FabX contains a [4Fe-4S] cluster essential for unsaturated fatty acid synthesis

Unsaturated fatty acids (UFAs) are essential for functional membrane phospholipids in most bacteria. The bifunctional dehydrogenase/isomerase FabX is an essential UFA biosynthesis enzyme in the widespread human pathogen Helicobacter pylori, a bacterium etiologically related to 95% of gastric cancers. Here, we present the crystal structures of FabX alone and in complexes with an octanoyl-acyl carrier protein (ACP) substrate or with holo-ACP. FabX belongs to the nitronate monooxygenase (NMO) flavoprotein family but contains an atypical [4Fe-4S] cluster absent in all other family members characterized to date. FabX binds ACP via its positively charged α7 helix that interacts with the negatively charged α2 and α3 helices of ACP. We demonstrate that the [4Fe-4S] cluster potentiates FMN oxidation during dehydrogenase catalysis, generating superoxide from an oxygen molecule that is locked in an oxyanion hole between the FMN and the active site residue His182. Both the [4Fe-4S] and FMN cofactors are essential for UFA synthesis, and the superoxide is subsequently excreted by H. pylori as a major resource of peroxide which may contribute to its pathogenic function in the corrosion of gastric mucosa.

In-Silico Studies on Selected Active Constituents of Corbichonia decumbens Against Allergic Bronchopulmonary Aspergillosis

Herbs have been employed in the treatment of various diseases and other medicinal purposes for a long time and they’ve been the zest of our life. Corbichonia decumbens an erect, short-lived succulent herb is found to possess zenith medicinal properties. At a first, the in-silico activity of the plant has been determined to carry out a modification in the Surfactant Protein-D (SP-D) which plays a pivotal role in defense against the Allergic Bronchopulmonary Aspergillosis (ABPA). The SP-D protein has been modified using in-silico tools thus making it more robust in containing ABPA. The protein SP-D when combined with the plant compound 1-methyl-3,5-dinitro-1,2,4-triazole had binding energy of -6.98 and interactions with active site residue ASN-236, LYS-246, GLU-232, PHE-234 and, GLN-236. Being one of the first in-silico works carried out in this plant species it aims to provide a substantial base for future works and unwrap the potential of this herb in all aspects of medicinal plant science.

Increasing Hydrolytic Activity of Lipase on Palm Oil by PCR-Based Random Mutagenesis

ABSTRACT Random mutagenesis technique is a powerful technique capable of producing enzymes with desired biocatalytic activity. This study aims to obtain a mutant lipase with improved hydrolytic activity on palm oil substrate using random mutagenesis technique. Random mutagenesis by error-prone PCR was used to generate mutant lipases. A total of 1101 mutants were obtained, out of which two mutants, Lip M14.25, and Lip M14.57, showed an increased relative hydrolytic activity. Lip M14.25 and Lip M14.57 demonstrated a 14% and 16% increased activity respectively. A comparison of the mutants' hydrolytic activities using p-nitrophenyl esters showed a significantly high preference for p-nitrophenyl palmitate. Furthermore, the mutant, Lip M14.25 showed its highest activity at pH 5, and Lip M14.57 exhibited a 10 oC decrease in optimum temperature. The two mutants' protein modelling showed the substitution of N44S/S202N on M14.25 and F154L/S265C on M14.57 lipase, which caused changes in conformation and active site residue distance of the lipase. The study found two mutants of lipase, M14.25 and M14.57, which showed improved hydrolytic activity on palm oil substrate.

Amino Acid Replacement at Position 228 Induces Fluctuation in the Ω-Loop of KPC-3 and Reduces the Affinity against Oxyimino Cephalosporins: Kinetic and Molecular Dynamics Studies

KPC enzymes are the most common class A carbapenemases globally diffused. The peculiarity of this family of β-lactamases is represented by their ability to hydrolyse all classes of β-lactams, including carbapenems, posing a serious problem to public health. In the present study, seven laboratory mutants of KPC-3 (D228S, D228W, D228M, D228K, D228L, D228I and D228G) were generated by site-saturation mutagenesis to explore the role of residue 228, a non-active site residue. Compared to KPC-3, the seven mutants showed evident differences in kcat and Km values calculated for some penicillins, cephalosporins and carbapenems. In particular, D228S and D228M showed a significant increase of Km values for cefotaxime and ceftazidime. Circular dichroism (CD) experiments have demonstrated that substitution at position 228 does not affect the secondary structure of the mutants. Molecular dynamics (MD) simulations were performed on KPC-3, D228S and D228M uncomplexed and complexed with cefotaxime (substrate). Although the residue 228 is located far from the active site, between α11 helix and β7 sheet in the opposite site of the Ω-loop, amino acid substitution at this position generates mechanical effects in the active site resulting in enzyme activity changes.

Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7

β-Glucosidases and β-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 β-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectively. Previous studies of crystal structures with glucoimidazole (GIm) and mannoimidazole (MIm) complexes and metadynamic simulations suggested that Os7BGlu26 hydrolyzes mannosides via the B2,5 transition state (TS) conformation preferred for mannosides and glucosides via their preferred 4H3/4E TS conformation. However, MIm is weakly bound by both enzymes. In the present study, we found that MIm was not bound in the active site of crystallized Os3BGlu7, but GIm was tightly bound in the −1 subsite in a 4H3/4E conformation via hydrogen bonds with the surrounding residues. One-microsecond molecular dynamics simulations showed that GIm was stably bound in the Os3BGlu7 active site and the glycone-binding site with little distortion. In contrast, MIm initialized in the B2,5 conformation rapidly relaxed to a E3/4H3 conformation and moved out into a position in the entrance of the active site, where it bound more stably despite making fewer interactions. The lack of MIm binding in the glycone site in protein crystals and simulations implies that the energy required to distort MIm to the B2,5 conformation for optimal active site residue interactions is sufficient to offset the energy of those interactions in Os3BGlu7. This balance between distortion and binding energy may also provide a rationale for glucosidase versus mannosidase specificity in plant β-glycosidases.