scholarly journals UbiD domain dynamics underpins aromatic decarboxylation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Stephen A. Marshall ◽  
Karl A. P. Payne ◽  
Karl Fisher ◽  
Gabriel R. Titchiner ◽  
Colin Levy ◽  
...  
Keyword(s):  
Active Site ◽  
Aromatic Compounds ◽  
Dipolar Cycloaddition ◽  
Acid Decarboxylase ◽  
Aromatic Moiety ◽  
Domain Motion ◽  
Viscosity Effects ◽  
Domain Dynamics ◽  
Covalent Catalysis ◽  
Allosteric Activator

AbstractThe widespread UbiD enzyme family utilises the prFMN cofactor to achieve reversible decarboxylation of acrylic and (hetero)aromatic compounds. The reaction with acrylic compounds based on reversible 1,3-dipolar cycloaddition between substrate and prFMN occurs within the confines of the active site. In contrast, during aromatic acid decarboxylation, substantial rearrangement of the substrate aromatic moiety associated with covalent catalysis presents a molecular dynamic challenge. Here we determine the crystal structures of the multi-subunit vanillic acid decarboxylase VdcCD. We demonstrate that the small VdcD subunit acts as an allosteric activator of the UbiD-like VdcC. Comparison of distinct VdcCD structures reveals domain motion of the prFMN-binding domain directly affects active site architecture. Docking of substrate and prFMN-adduct species reveals active site reorganisation coupled to domain motion supports rearrangement of the substrate aromatic moiety. Together with kinetic solvent viscosity effects, this establishes prFMN covalent catalysis of aromatic (de)carboxylation is afforded by UbiD dynamics.

Introduction of Perfluoroalkyl Substituents into Heteroarenes via Nucleophilic Substitution of Hydrogen

2008 ◽  
Vol 63 (4) ◽  
pp. 363-374 ◽  
Author(s):  
Mieczysław Mąkosza ◽  
Rafał Loska
Keyword(s):  
Nucleophilic Substitution ◽  
Aromatic Compounds ◽  
Dipolar Cycloaddition ◽  
Nucleophilic Substitution Of Hydrogen ◽  
Hydrogen Addition ◽  
Reaction With Water ◽  
Acid Fluorides

AbstractA summary of research in the area of fluoroalkylation of electron-deficient aromatic compounds is presented. The reaction of dinitro- and cyanonitroarenes with trifluoromethyl-trimethylsilane (Me3SiCF3) and tris(dimethylamino)sulfonium difluorotrimethylsilicate (TASF) and subsequently with DMD provides trifluoromethylated cyano- and nitrophenols via oxidative nucleophilic substitution of hydrogen. Addition of fluorinated carbanions, generated either by addition of F− anions to hexafluoropropene or by activation of Me3SiCF3, to N-alkylazinium salts leads to dihydropyridines, dihydroquinolines etc., oxidation of which affords the respective fluoroalkylated heterocycles.1,3-Dipolar cycloaddition of azine N-oxides to hexafluoropropene gives 2-heteroaryl-2,3,3,3-tetrafluoropropionic acid fluorides, which react with various protic nucleophiles to give esters and amides of 2-heteroarylperfluoropropionic acids, whereas reaction with water and decarboxylation of the free acids gives azines with a 1,2,2,2-tetrafluoroethyl group at C-2.

scholarly journals Formation of N-hydroxy-N-arylacetamides from nitroso aromatic compounds by the mammalian pyruvate dehydrogenase complex

1993 ◽  
Vol 290 (3) ◽  
pp. 783-790 ◽  
Author(s):  
T Yoshioka ◽  
T Uematsu
Keyword(s):  
Pyruvate Dehydrogenase ◽  
Active Site ◽  
Aromatic Compounds ◽  
Pyruvate Dehydrogenase Complex ◽  
Catalytic Efficiency ◽  
Nitroso Compounds ◽  
Factors Affecting ◽  
Porcine Heart ◽  
Alkyl Groups ◽  
Dehydrogenase Complex

Bovine, human and porcine heart mitochondria and isolated porcine heart pyruvate dehydrogenase complex (PDHC) pyruvate-dependently form N-hydroxy-N-arylacetamides from nitroso aromatic compounds, including carcinogenic 4-biphenyl and 2-fluorenyl derivatives. The PDHC-catalysed formation of N-hydroxyacetanilide (N-OH-AA) from nitrosobenzene (NOB), through a Ping Pong mechanism, is optimum at pH 6.8 and is accelerated by thiamin pyrophosphate, but is inhibited by thiamin thiazolone pyrophosphate and ATP. Km pyruvate in the reaction is independent of pH over the range tested, whereas KmNOB increases at lower pH, owing to ionization of an active-site functional group of pKa 6.3. The enzymic ionization decreases log (Vmax/KmNOB). Isolated pyruvate dehydrogenase (E1), a constitutive enzyme of PDHC, forms N-OH-AA by itself and has comparable kinetic parameters to those of the PDHC-catalysed N-OH-AA formation. The catalytic efficiency of PDHC in the formation of N-hydroxy-N-arylacylamides, due to the steric limitation of the active site of E1, is lowered both by bulky alkyl groups of alpha-oxo acids and by p-substituents (but not an o-substituent) on nitrosobenzenes. These nitroso compounds serve as electrophiles in the reaction in which the reductive acetylation step is rate-limiting. The reaction mechanism and other factors affecting N-hydroxy-N-arylacylamide formation are discussed.

scholarly journals Novel 3,6-Dihydroxypicolinic Acid Decarboxylase Mediated Picolinic Acid Catabolism inAlcaligenes faecalisJQ135

2018 ◽  
Author(s):  
Qiu Jiguo ◽  
Zhang Yanting ◽  
Yao Shigang ◽  
Ren Hao ◽  
Qian Meng ◽  
...  
Keyword(s):  
Aromatic Compounds ◽  
Picolinic Acid ◽  
Degradation Pathway ◽  
Site Directed Mutagenesis ◽  
Acid Decarboxylase ◽  
Directed Mutagenesis ◽  
Deficient Mutant ◽  
Carbon And Nitrogen ◽  
Genetic Deletion ◽  
Related Proteins

AbstractAlcaligenesfaecalisstrain JQ135 utilizes picolinic acid (PA) as sole carbon and nitrogen source for growth. In this study, we screened a 6-hydroxypicolinic acid (6HPA) degradation-deficient mutant through random transposon mutagenesis. The mutant hydroxylated 6HPA into an intermediate, identified as 3,6-dihydroxypicolinic acid (3,6DHPA) with no further degradation. A novel decarboxylase PicC was identified that was found to be responsible for the decarboxylation of 3,6DHPA to 2.5-dihydroxypyridine. Although, PicC belonged to amidohydrolase_2 family, it shows low similarity (<45%) when compared to other reported amidohydrolase_2 family decarboxylases. Moreover, PicC was found to form a monophyletic group in the phylogenetic tree constructed using PicC and related proteins. Further, the genetic deletion and complementation results demonstrated thatpicCwas essential for PA degradation. The PicC was Zn2+-dependent non-oxidative decarboxylase that can specifically catalyze the irreversible decarboxylation of 3,6DHPA to 2.5-dihydroxypyridine. TheKmandkcattowards 3,6DHPA were observed to be 13.44 μM and 4.77 s-1, respectively. Site-directed mutagenesis showed that His163 and His216 were essential for PicC activity.ImportancePicolinic acid is a natural toxic pyridine derived from L-tryptophan metabolism and some aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize picolinic acid for their growth, and thus, a microbial degradation pathway of picolinic acid has been proposed. Picolinic acid is converted into 6-hydroxypicolinic acid, 3,6-dihydroxypicolinic acid, and 2,5-dihydroxypyridine in turn. However, there was no physiological and genetic validation for this pathway. This study demonstrated that 3,6DHPA was an intermediate in PA catabolism process and further identified and characterized a novel amidohydrolase_2 family decarboxylase PicC. It was also shown that PicC could catalyze the decarboxylation process of 3,6-dihydroxypicolinic acid into 2,5-dihydroxypyridine. This study provides a basis for understanding PA degradation pathway and the underlying molecular mechanism.

scholarly journals Structure and substrate specificity determinants of the taurine biosynthetic enzyme cysteine sulphinic acid decarboxylase

2020 ◽  
Author(s):  
Elaheh Mahootchi ◽  
Arne Raasakka ◽  
Weisha Luan ◽  
Gopinath Muruganandam ◽  
Remy Loris ◽  
...  
Keyword(s):  
Amino Acid ◽  
Substrate Specificity ◽  
Active Site ◽  
Ph Regulation ◽  
Enzymatic Oxidation ◽  
Acid Decarboxylase ◽  
Critical Determinant ◽  
Signalling Molecules ◽  
Binding Cavity ◽  
Abundant Amino Acid

AbstractPyridoxal 5′-phosphate (PLP) is an important cofactor for amino acid decarboxylases with many biological functions, including the synthesis of signalling molecules, such as serotonin, dopamine, histamine, γ-aminobutyric acid, and taurine. Taurine is an abundant amino acid with multiple physiological functions, including osmoregulation, pH regulation, antioxidative protection, and neuromodulation. In mammalian tissues, taurine is mainly produced by decarboxylation of cysteine sulphinic acid to hypotaurine, catalysed by the PLP-dependent cysteine sulphinic acid decarboxylase (CSAD), followed by non-enzymatic oxidation of the product to taurine. We determined the crystal structure of mouse CSAD and compared it to other PLP-dependent decarboxylases in order to identify determinants of substrate specificity and catalytic activity. Recognition of the substrate involves distinct side chains forming the substrate-binding cavity. In addition, the backbone conformation of a buried active-site loop appears to be a critical determinant for substrate side chain binding in PLP-dependent decarboxylases. Phe94 was predicted to affect substrate specificity, and its mutation to serine altered both the catalytic properties of CSAD and its stability. Using small-angle X-ray scattering, we further showed that similarly to its closest homologue, GADL1, CSAD presents open/close motions in solution. The structure of apo-CSAD indicates that the active site gets more ordered upon internal aldimine formation. Taken together, the results highlight details of substrate recognition in PLP-dependent decarboxylases and provide starting points for structure-based inhibitor design with the aim of affecting the biosynthesis of taurine and other abundant amino acid metabolites.

scholarly journals Novel 3,6-Dihydroxypicolinic Acid Decarboxylase-Mediated Picolinic Acid Catabolism inAlcaligenes faecalisJQ135

2019 ◽  
Vol 201 (7) ◽  
Author(s):  
Jiguo Qiu ◽  
Yanting Zhang ◽  
Shigang Yao ◽  
Hao Ren ◽  
Meng Qian ◽  
...  
Keyword(s):  
Aromatic Compounds ◽  
Picolinic Acid ◽  
Alcaligenes Faecalis ◽  
Degradation Pathway ◽  
Site Directed Mutagenesis ◽  
Pyridine Derivative ◽  
Acid Decarboxylase ◽  
Microbial Cells ◽  
Content Type ◽  
Related Proteins

ABSTRACTPicolinic acid (PA), a typical C-2-carboxylated pyridine derivative, is a metabolite ofl-tryptophan and many other aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize PA for growth. However, the precise mechanism of PA metabolism remains unknown.Alcaligenes faecalisstrain JQ135 utilizes PA as its carbon and nitrogen source for growth. In this study, we screened a 6-hydroxypicolinic acid (6HPA) degradation-deficient mutant through random transposon mutagenesis. The mutant hydroxylated 6HPA into an intermediate, identified as 3,6-dihydroxypicolinic acid (3,6DHPA), with no further degradation. A novel decarboxylase, PicC, was identified to be responsible for the decarboxylation of 3,6DHPA to 2,5-dihydroxypyridine. Although, PicC belonged to the amidohydrolase 2 family, it shows low similarity (<45%) compared to other reported amidohydrolase 2 family decarboxylases. Moreover, PicC was found to form a monophyletic group in the phylogenetic tree constructed using PicC and related proteins. Further, the genetic deletion and complementation results demonstrated thatpicCwas essential for PA degradation. The PicC was Zn2+-dependent nonoxidative decarboxylase that can specifically catalyze the irreversible decarboxylation of 3,6DHPA to 2,5-dihydroxypyridine. TheKmandkcattoward 3,6DHPA were observed to be 13.44 μM and 4.77 s−1, respectively. Site-directed mutagenesis showed that His163 and His216 were essential for PicC activity. This study provides new insights into the microbial metabolism of PA at molecular level.IMPORTANCEPicolinic acid is a natural toxic pyridine derived froml-tryptophan metabolism and other aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize picolinic acid for their growth, and thus a microbial degradation pathway of picolinic acid has been proposed. Picolinic acid is converted into 6-hydroxypicolinic acid, 3,6-dihydroxypicolinic acid, and 2,5-dihydroxypyridine in turn. However, there was no physiological and genetic validation for this pathway. This study demonstrated that 3,6-dihydroxypicolinic acid was an intermediate in picolinic acid catabolism and further identified and characterized a novel amidohydrolase 2 family decarboxylase PicC. PicC was also shown to catalyze the decarboxylation of 3,6-dihydroxypicolinic acid into 2,5-dihydroxypyridine. This study provides a basis for understanding picolinic acid degradation and its underlying molecular mechanism.

scholarly journals Factors that influence the translocation of the N-carboxybiotin moiety between the two sub-sites of pyruvate carboxylase

1981 ◽  
Vol 199 (3) ◽  
pp. 603-609 ◽  
Author(s):  
G J Goodall ◽  
G S Baldwin ◽  
J C Wallace ◽  
D B Keech
Keyword(s):  
Dissociation Constant ◽  
Carboxy Group ◽  
Active Site ◽  
Pyruvate Carboxylase ◽  
Alternative Substrate ◽  
Acetyl Coa ◽  
Low Concentrations ◽  
Acid Substrate ◽  
Allosteric Activator ◽  
Rate Of Movement

The active site of pyruvate carboxylase, like those of all biotin-dependent carboxylases, is believed to consist of two spatially distinct sub-sites with biotin acting as a mobile carboxy-group carrier oscillating between the two sub-sites. Some of the factors that influence the location and rate of movement of the N-carboxybiotin were studied. The rate of carboxylation of the alternative substrate, 2-oxobutyrate, was measured at 0 degrees C in an assay system where the isolated enzyme--[14C]carboxybiotin was the carboxy-group donor. The results are consistent with the hypothesis that the location of the carboxybiotin in the active site is determined by the presence of Mg2+, acetyl-CoA and the oxo acid substrate. The presence of Mg2+ favours the holding of the complex at the first sub-site, whereas alpha-oxo acids induce the complex to move to the second sub-site. At low concentrations pyruvate induces this movement but does not efficiently act as a carboxy-group acceptor; hydroxypyruvate, glyoxylate and oxamate, though not carboxylated, still induce the movement. The allosteric activator acetyl-CoA exerts only a slight stimulation on the rate of translocation to the second sub-site, and this stimulation arises from an increase in the dissociation constant for Mg2+.

Phosphofructokinase: structure and control

1981 ◽  
Vol 293 (1063) ◽  
pp. 53-62 ◽  
Keyword(s):  
Active Site ◽  
Binding Sites ◽  
Bacillus Stearothermophilus ◽  
Phosphoryl Transfer ◽  
Active Conformation ◽  
Allosteric Activation ◽  
Ligand Binding Sites ◽  
And Control ◽  
Allosteric Activator ◽  
Cooperative Kinetics

Phosphofructokinase from Bacillus stearothermophilus shows cooperative kinetics with respect to the substrate fructose-6-phosphate (F6P), allosteric activation by ADP, and inhibition by phosphoenolpyruvate. The crystal structure of the active conformation of the enzyme has been solved to 2.4 A resolution, and three ligand-binding sites have been located. Two of these form the active site and bind the substrates F6P and ATP. The third site binds both allosteric activator and inhibitor. The complex of the enzyme with F6P and ADP has been partly refined at 2.4 A resolution, and a model of ATP has been built into the active site by using the refined model of ADP and a 6 A resolution map of bound 5'-adenylylimidodiphosphate (AMPPNP). The y-phosphate of ATP is close to the 1-hydroxyl of F6P, in a suitable position for in-line phosphoryl transfer. The binding of the phosphate of F6P involves two arginines from a neighbouring subunit in the tetramer, which suggests that a rearrangement of the subunits could explain the cooperativity of substrate binding. The activator ADP is also bound by residues from two subunits.

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