scholarly journals Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites

2019 ◽  
Vol 116 (51) ◽  
pp. 25583-25590 ◽  
Author(s):  
Jethro L. Hemmann ◽  
Tristan Wagner ◽  
Seigo Shima ◽  
Julia A. Vorholt
Keyword(s):  
Active Sites ◽  
Bacterial Species ◽  
Methanogenic Archaea ◽  
Side Chain ◽  
Strong Interactions ◽  
Prosthetic Group ◽  
Additional Function ◽  
Amide Bonds ◽  
Consecutive Reactions ◽  
The One

Methylotrophy, the ability of microorganisms to grow on reduced one-carbon substrates such as methane or methanol, is a feature of various bacterial species. The prevailing oxidation pathway depends on tetrahydromethanopterin (H4MPT) and methylofuran (MYFR), an analog of methanofuran from methanogenic archaea. Formyltransferase/hydrolase complex (Fhc) generates formate from formyl-H4MPT in two consecutive reactions where MYFR acts as a carrier of one-carbon units. Recently, we chemically characterized MYFR from the model methylotrophMethylorubrum extorquensand identified an unusually long polyglutamate side chain of up to 24 glutamates. Here, we report on the crystal structure of Fhc to investigate the function of the polyglutamate side chain in MYFR and the relatedness of the enzyme complex with the orthologous enzymes in archaea. We identified MYFR as a prosthetic group that is tightly, but noncovalently, bound to Fhc. Surprisingly, the structure of Fhc together with MYFR revealed that the polyglutamate side chain of MYFR is branched and contains glutamates with amide bonds at both their α- and γ-carboxyl groups. This negatively charged and branched polyglutamate side chain interacts with a cluster of conserved positively charged residues of Fhc, allowing for strong interactions. The MYFR binding site is located equidistantly from the active site of the formyltransferase (FhcD) and metallo-hydrolase (FhcA). The polyglutamate serves therefore an additional function as a swinging linker to shuttle the one-carbon carrying amine between the two active sites, thereby likely increasing overall catalysis while decreasing the need for high intracellular MYFR concentrations.

scholarly journals Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-l-fucosidases from GH29

2018 ◽  
Vol 293 (47) ◽  
pp. 18296-18308 ◽  
Author(s):  
Chelsea Vickers ◽  
Feng Liu ◽  
Kento Abe ◽  
Orly Salama-Alber ◽  
Meredith Jenkins ◽  
...  
Keyword(s):  
Glycoside Hydrolase ◽  
Biological Activities ◽  
Bacterial Species ◽  
Structural Data ◽  
Side Chain ◽  
Glycoside Hydrolase Family ◽  
X Ray Crystallography ◽  
Catalytic Mechanisms ◽  
Thickening Agents ◽  
Hydrolase Family

Fucoidans are chemically complex and highly heterogeneous sulfated marine fucans from brown macro algae. Possessing a variety of physicochemical and biological activities, fucoidans are used as gelling and thickening agents in the food industry and have anticoagulant, antiviral, antitumor, antibacterial, and immune activities. Although fucoidan-depolymerizing enzymes have been identified, the molecular basis of their activity on these chemically complex polysaccharides remains largely uninvestigated. In this study, we focused on three glycoside hydrolase family 107 (GH107) enzymes: MfFcnA and two newly identified members, P5AFcnA and P19DFcnA, from a bacterial species of the genus Psychromonas. Using carbohydrate-PAGE, we show that P5AFcnA and P19DFcnA are active on fucoidans that differ from those depolymerized by MfFcnA, revealing differential substrate specificity within the GH107 family. Using a combination of X-ray crystallography and NMR analyses, we further show that GH107 family enzymes share features of their structures and catalytic mechanisms with GH29 α-l-fucosidases. However, we found that GH107 enzymes have the distinction of utilizing a histidine side chain as the proposed acid/base catalyst in its retaining mechanism. Further interpretation of the structural data indicated that the active-site architectures within this family are highly variable, likely reflecting the specificity of GH107 enzymes for different fucoidan substructures. Together, these findings begin to illuminate the molecular details underpinning the biological processing of fucoidans.

Catalytic activity of CuGHK peptide-based porous material

2021 ◽  
Author(s):  
Francisco G. Cirujano ◽  
Nuria Martin ◽  
Neyvis Almora-Barrios ◽  
Carlos Martí-Gastaldo
Keyword(s):  
Catalytic Activity ◽  
Porous Material ◽  
Active Sites ◽  
Room Temperature ◽  
Side Chain ◽  
Periodic Distribution ◽  
Lysine Side Chain ◽  
One Step

Room temperature one-step synthesis of the peptide-based porous material with a periodic distribution of pockets decorated with lysine side chain active sites behaves as a heterogeneous organocatalyst. The pockets are...

The significance of the Cα substituent in the selective inhibition of matrix metalloproteinases 1 and 9

2011 ◽  
Vol 392 (11) ◽  
Author(s):  
Riyad Domingo ◽  
Kelly Chibale ◽  
Edward D. Sturrock
Keyword(s):  
Hydrogen Bonding ◽  
Matrix Metalloproteinases ◽  
Active Sites ◽  
Unsaturated Compound ◽  
Selective Inhibition ◽  
Acid Group ◽  
Side Chain ◽  
Carboxylic Acid Group ◽  
Lead Compounds ◽  
Hydrogen Bonding Interactions

Abstract Matrix metalloproteinases (MMPs) cleave and degrade most components of the extracellular matrix, and unregulated MMP activity has been correlated to cancer and metastasis. Hence there is a burgeoning need to develop inhibitors that bind selectively to structurally similar MMPs. The inhibition profiles of peptidomimetics containing Cα substituents at the α,β unsaturated carbon were evaluated against the recombinant forms of ADAM17, MMP1, and MMP9. The dicarboxylic acid D2 and hydroxamate C2 inhibited MMP9 but not MMP1. The unsaturated compound E2 displayed selective inhibition for MMP1, compared with the saturated precursor C2, with an IC50 value of 3.91 μm. The molecular basis for this selectivity was further investigated by the molecular docking of E2 and D2 into the active sites of MMP1 and MMP9. These data demonstrate hydrogen-bonding interactions between the carbonyl group of the Cα substituent of E2 and the side chain of Asn180 present in the active site of MMP1. Conversely, the docked MMP9-D2 structure shows hydrophobic and hydrogen bonding between the ligand’s morpholine substituent and second carboxylic acid group with Leu187 and an amide, respectively. This study suggests that substituents other than P1′ and P2′ may confer selectivity among MMPs and may aid in the search for novel lead compounds.

scholarly journals Cost-Effective Fabrication, Antibacterial Application and Cell Viability Studies of Modified Nonwoven Cotton Fabric

2021 ◽  
Author(s):  
Rahat Nawaz ◽  
Sayed Tayyab Raza Naqvi ◽  
Batool Fatima ◽  
Nazia Zulfiqar ◽  
Muhammad Umer Farooq ◽  
...  
Keyword(s):  
Cotton Fabric ◽  
Biomedical Applications ◽  
Active Sites ◽  
Food Packaging ◽  
Low Cost ◽  
Bacterial Species ◽  
Enterobacter Aerogenes ◽  
Cost Effective ◽  
Bacterial Strains ◽  
Toxicity Assay

Abstract Nonwoven cotton fabric has been fabricated and designed for antibacterial applications using low cost and ecofriendly precursors. The treatment of fabric with alkali leads to formation of active sites. The surfaces were dip coated with silver nanaoparticles and chitosan. The surface was chlorinated in next step to transform amide (N-H) groups in chitosan into N-halamine (N-Cl). The modified and unmodified surfaces of the nonwoven cotton fabric have been characterized by FTIR, SEM, and XRD. The active chlorine loading is measured with iodine/ sodium thiosulphate. The antimicrobial activity and cell toxicity assay were carried out with and without modifications of nonwoven cotton fabric. The antimicrobial efficacies of loaded fabric were evaluated against four bacterial species (Micrococcus lutes, Staphylococcus aurea, Enterobacter aerogenes, and E.coli). It was found that modified fabric exhibited superior efficiency against gram-positive and gram-negative bacterial strains as compared to their bulk counterparts upon exposure without destroying and affecting fabric nature. The overall process is economical for commercial purposes. The modified fabric can be used for antimicrobial, health, and food packaging industries, and in other biomedical applications.

The tert-Butyl Side Chain: A Powerful Means to Lock Peptoid Amide Bonds in the Cis Conformation

2013 ◽  
Vol 15 (9) ◽  
pp. 2246-2249 ◽  
Author(s):  
O. Roy ◽  
C. Caumes ◽  
Y. Esvan ◽  
C. Didierjean ◽  
S. Faure ◽  
...  
Keyword(s):  
Side Chain ◽  
Amide Bonds ◽  
Tert Butyl ◽  
Powerful Means

scholarly journals Bacteriophages and the One Health Approach to Combat Multidrug Resistance: Is This the Way?

Antibiotics ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 414
Author(s):  
Mary Garvey
Keyword(s):  
Large Scale ◽  
One Health ◽  
Bacterial Resistance ◽  
Therapeutic Potential ◽  
Methicillin Resistance ◽  
Bacterial Species ◽  
Emerging Diseases ◽  
Scale Production ◽  
Essential Components ◽  
The One

Antimicrobial resistance necessitates action to reduce and eliminate infectious disease, ensure animal and human health, and combat emerging diseases. Species such as Acinetobacter baumanniii, vancomycin resistant Enterococcus, methicillin resistance Staphylococcus aureus, and Pseudomonas aeruginosa, as well as other WHO priority pathogens, are becoming extremely difficult to treat. In 2017, the EU adopted the “One Health” approach to combat antibiotic resistance in animal and human medicine and to prevent the transmission of zoonotic disease. As the current therapeutic agents become increasingly inadequate, there is a dire need to establish novel methods of treatment under this One Health Framework. Bacteriophages (phages), viruses infecting bacterial species, demonstrate clear antimicrobial activity against an array of resistant species, with high levels of specificity and potency. Bacteriophages play key roles in bacterial evolution and are essential components of all ecosystems, including the human microbiome. Factors such are their specificity, potency, biocompatibility, and bactericidal activity make them desirable options as therapeutics. Issues remain, however, relating to their large-scale production, formulation, stability, and bacterial resistance, limiting their implementation globally. Phages used in therapy must be virulent, purified, and well characterized before administration. Clinical studies are warranted to assess the in vivo pharmacokinetics and pharmacodynamic characteristics of phages to fully establish their therapeutic potential.

scholarly journals An alkylaminoquinazoline restores antibiotic activity in Gram-negative resistant isolates

Microbiology ◽  
2011 ◽  
Vol 157 (2) ◽  
pp. 566-571 ◽  
Author(s):  
Abdallah Mahamoud ◽  
Jacqueline Chevalier ◽  
Milad Baitiche ◽  
Elissavet Adam ◽  
Jean-Marie Pagès
Keyword(s):  
Efflux Pump ◽  
Bacterial Species ◽  
Efflux Pumps ◽  
Multidrug Resistant ◽  
Side Chain ◽  
Structural Class ◽  
Gram Negative ◽  
Activity Spectrum ◽  
Efflux Pump Inhibitors ◽  
Drug Efflux Pump

To date, various bacterial drug efflux pump inhibitors (EPIs) have been described. They exhibit variability in their activity spectrum with respect to antibiotic structural class and bacterial species. Among the various 4-alkylaminoquinazoline derivatives synthesized and studied in this work, one molecule, 1167, increased the susceptibility of important human-pathogenic, resistant, Gram-negative bacteria towards different antibiotic classes. This 4-(3-morpholinopropylamino)-quinazoline induced an increase in the activity of chloramphenicol, nalidixic acid, norfloxacin and sparfloxacin, which are substrates of the AcrAB-TolC and MexAB-OprM efflux pumps that act in these multidrug-resistant isolates. In addition, 1167 increased the intracellular concentration of chloramphenicol in efflux pump-overproducing strains. The rate of restoration depended on the structure of the antibiotic, suggesting that different sites in the efflux pumps may be involved. A molecule exhibiting a morpholine functional group and a propyl extension of the side chain was more active.

Reduction of Cell Lysate Viscosity during Processing of Poly(3-Hydroxyalkanoates) by Chromosomal Integration of the Staphylococcal Nuclease Gene in Pseudomonas putida

1999 ◽  
Vol 65 (4) ◽  
pp. 1524-1529 ◽  
Author(s):  
Zhuang L. Boynton ◽  
Joseph J. Koon ◽  
Elaine M. Brennan ◽  
Jeralyn D. Clouart ◽  
Daniel M. Horowitz ◽  
...  
Keyword(s):  
Pseudomonas Putida ◽  
Ralstonia Eutropha ◽  
Bacterial Species ◽  
Downstream Processing ◽  
Staphylococcal Nuclease ◽  
Side Chain ◽  
Chromosomal Dna ◽  
Industrial Processing ◽  
Film Forming ◽  
High Cell Density Cultures

ABSTRACT Poly(3-hydroxyalkanoates) (PHAs) are biodegradable thermoplastics which are accumulated by many bacterial species in the form of intracellular granules and which are thought to serve as reserves of carbon and energy. Pseudomonas putida accumulates a polyester, composed of medium-side-chain 3-hydroxyalkanoic acids, which has excellent film-forming properties. Industrial processing of PHA involves purification of the PHA granules from high-cell-density cultures. After the fermentation process, cells are lysed by homogenization and PHA granules are purified by chemical treatment and repeated washings to yield a PHA latex. Unfortunately, the liberation of chromosomal DNA during lysis causes a dramatic increase in viscosity, which is problematic in the subsequent purification steps. Reduction of the viscosity is generally achieved by the supplementation of commercially available nuclease preparations or by heat treatment; however, both procedures add substantial costs to the process. As a solution to this problem, a nuclease-encoding gene fromStaphylococcus aureus was integrated into the genomes of several PHA producers. Staphylococcal nuclease is readily expressed in PHA-producing Pseudomonas strains and is directed to the periplasm, and occasionally to the culture medium, without affecting PHA production or strain stability. During downstream processing, the viscosity of the lysate from a nuclease-integratedPseudomonas strain was reduced to a level similar to that observed for the wild-type strain after treatment with commercial nuclease. The nuclease gene was also functionally integrated into the chromosomes of other PHA producers, including Ralstonia eutropha.

scholarly journals Comparison in thermal stability and catalytic performance of H4PMo11VO40 heteropolyacid supported on mesoporous and macroporous silica materials

2020 ◽  
pp. 174751982092599
Author(s):  
Heng Zhang ◽  
Chunhao Yang ◽  
Shengying Zhao ◽  
Tingting Wang ◽  
Wancheng Zhu
Keyword(s):  
Thermal Stability ◽  
Active Sites ◽  
Catalytic Performance ◽  
High Dispersion ◽  
High Exposure ◽  
Macroporous Silica ◽  
One Dimensional ◽  
Ordered Macroporous ◽  
The One ◽  
Mcm 41

Ordered mesoporous silica, SBA-15 and MCM-41, and three-dimensionally ordered macroporous SiO2 were used as the supports of H4PMo11VO40 heteropolyacid for methacrolein oxidation. The dispersion and structural evolutions of the heteropolyacid along with thermal treatment were investigated. It was found that the heteropolyacid entered the one-dimensional mesoporous channels of SBA-15 and MCM-41, and the crystallization and growth were limited, leading to high dispersion of the heteropolyacid. However, the thermal stability was decreased under high dispersion. The migration of the heteropolyacid was observed to the end of the one-dimensional channels of SBA-15 and the outer surface of MCM-41 with calcination, accompanied by the decomposition of the heteropolyacid and the formation of MoO3. In comparison, the crystallization and growth of heteropolyacid were not limited in the open macropores of three-dimensionally ordered macroporous SiO2. Dispersed particles on the surface of the macropores with size of about 5 nm exhibited a higher thermal stability. The decomposition of the heteropolyacid in the SBA-15 and MCM-41 supported catalysts resulted in the loss of strong acid sites, causing low selectivity to methacrylic acid in methacrolein oxidation. High thermal stability with high exposure of the active sites in the three-dimensionally ordered macroporous SiO2 supported catalyst contributed to the enhancement in the catalytic performance.

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