Enzyme catalysis

Piper betle Linn. (Piperaceae) commonly known as betel vine is a popular medicinal plant in Asia.[1] Piper betle leaves have been used as a traditional medicine to treat a variety of health conditions thanks to their antibacterial, antifungal and antioxidant properties.

7p vikwong 29-09-2024 4 1   Download

Nicotinamide N-methyltransferase (NNMT), a key cytoplasmic protein in the human body, is accountable to catalyze the nicotinamide (NCA) N1 -methylation through S-adenosyl-L-methionine (SAM) as a methyl donor, which has been linked to many diseases. Although extensive studies have concerned about the biological aspect, the detailed mechanism study of the enzyme function, especially in the part of protein dynamics is lacking.

9p thiencuuchu 27-11-2021 17 2   Download

This review describes studies of particular enzymatically catalyzed reactions to investigate the possibility that catalysis is mediated by protein dynamics. That is, evolution has crafted the protein backbone of the enzyme to direct vibrations in such a fashion to speed reaction. The review presents the theoretical approach we have used to investigate this problem, but it is designed for the nonspecialist.

10p system191 01-06-2013 36 4   Download

Recent years have witnessed high levels of activity in identifying enzyme systems that catalyse H-transfer by quantum tunneling. Rather than being restricted to a small number of specific enzymes as perceived initially, it has now become an accepted mechanism for H-transfer in a growing number of enzymes. Furthermore, H-tunneling is driven by the thermally induced dynamics of the enzyme. In some of those enzymes that break stable C–H bonds the reaction proceeds purely by quantum tunneling, without the need to partially ascend the barrier.

7p system191 01-06-2013 40 3   Download

The plant enzyme phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) shows homology to histidine ammonia-lyase (HAL) whose structure has been solved by X-ray crystallography. Based on amino-acid sequence alignment of the two enzymes, mutagenesis was performed on amino-acid residues that were identical or similar to the active site residues in HAL to gain insight into the importance of this residues in PAL for substrate binding or catalysis. We mutated the following amino-acid residues: S203, R354, Y110, Y351, N260, Q348, F400, Q488 and L138....

11p system191 01-06-2013 64 4   Download

Mikrobiologisches Institut der Eidgeno¨ssischen Technischen Hochschule, ETH-Zentrum, Zu¨rich, Switzerland The membrane-bound b subunit of the oxaloacetate decarboxylase Na+ pump of Klebsiella pneumoniae catalyzes the decarboxylation of enzyme-bound biotin. This event is coupled to the transport of 2 Na+ ions into the periplasm and consumes a periplasmically derived proton. The connecting fragment IIIa and transmembrane helices IV and VIII of the b subunit are highly conserved, harboring residues D203, Y229, N373, G377, S382, and R389 that play a profound role in catalysis. ...

8p system191 01-06-2013 33 4   Download

Hevamine is a chitinase from the rubber tree Hevea brasiliensis. Its active site contains Asp125, Glu127, and Tyr183, which interact with the )1 sugar residue of the substrate. To investigate their role in catalysis, we have successfully expressed wild-type enzyme and mutants of these residues as inclusion bodies in Escherichia coli. After refolding and purification they were characterized by both structural and enzyme kinetic studies. Mutation of Tyr183 to phenylalanine produced an enzyme with a lower kcat and a slightly higher Km than the wild-type enzyme.

9p research12 01-06-2013 48 4   Download

DNA ligases are the enzymes responsible for the repair of single-strandedanddouble-strandednicks indsDNA.DNA ligases are structurally similar, possibly sharing a common molecular mechanism of nick recognition and ligation catalysis. This mechanism remains unclear, in part because the structure of ligase in complex with dsDNAhas yet to be solved.DNA ligases share common structural elementswith DNA polymerases, which have been cocrystallized with dsDNA. Based on the observed DNA polymerase–dsDNA interactions, we propose a mechanism for recognition of a single-stranded nick by DNA ligase....

7p tumor12 22-04-2013 39 2   Download

CYP73 enzymes are highly conserved cytochromes P450 in plant species that catalyse the regiospecific 4-hydroxylation ofcinnamicacid to formprecursorsofligninandmanyother phenolic compounds. A CYP73A1 homology model based on P450 experimentally solved structures was used to iden-tify active site residues likely togovern substrate binding and regio-specific catalysis. The functional significance of these residues was assessed using site-directedmutagenesis.

12p tumor12 20-04-2013 40 3   Download

The gene encodingBacillus subtilisUMP kinase (pyrH/ smbA) is transcribed in vivo into a functional enzyme, which represents approximately 0.1% of total soluble proteins. The specific activity of the purified enzyme under optimal conditions is 25 unitsÆmg )1 of protein. In the absenceofGTP,theactivityofB. subtilisenzyme is less than 10% of its maximum activity. Only dGTP and 3¢-anthraniloyl-2¢-deoxyguanosine-5¢-triphosphate (Ant-dGTP) can increase catalysis significantly.

9p tumor12 20-04-2013 33 2   Download

Limitedproteolysis of the pyruvate decarboxylase (E1,a2b2 ) component of the pyruvate dehydrogenase (PDH) multi-enzyme complexofBacillus stearothermophilushas indicated the importance for catalysis of a site (Tyr281-Arg282) in the E1asubunit (Chauhan, H.J., Domingo, G.J., Jung, H.-I. & Perham, R.N. (2000)Eur. J. Biochem.267, 7158–7169). This site appears to be conserved in the a-subunit of hetero-tetrameric E1s and multiple sequence alignments suggest that there are additional conserved amino-acid residues in this region, part of a common pattern with the consensus sequence -YR-H-D-YR-DE-.

10p tumor12 20-04-2013 54 3   Download

Butyrylcholinesterase is a serine esterase, closely related to acetylcholinesterase. Both enzymes employ a catalytic triad mechanism for catalysis, similar to that used by serine pro-teases such as a-chymotrypsin. Enzymes of this type are generally considered to be inactive at pH values below 5, because the histidine member of the catalytic triad becomes protonated. We have found that butyrylcholinesterase retains activity at pH £ 5, under conditions of excess substrate activation.

10p tumor12 20-04-2013 25 4   Download

hort hydrogen bonds are present in many chemical and biological sys-tems. It is well known that these short hydrogen bonds are found in the active site of enzymes and aid enzyme catalysis. This study aims to system-atically characterize all short hydrogen bonds from a nonredundant dataset of protein structures. The study has revealed that short hydrogen bonds are commonly found in proteins and are widely present in different regions of the protein chain, such as the backbone or side chain, and in different secondary structural regions such as helices, strands and turns. ...

14p awards 06-04-2013 43 3   Download

Transketolase from baker’s yeast is a thiamin diphosphate-dependent enzyme in sugar metabolism that reconstitutes with various analogues of the coenzyme. The methylated analogues (4¢-methylamino-thiamin diphos-phate and N1¢-methylated thiamin diphosphate) of the native cofactor were used to investigate the function of the aminopyrimidine moiety of the coen-zyme in transketolase catalysis.

17p awards 06-04-2013 38 4   Download

Family 18 chitinases such as chitinase B (ChiB) fromSerratia marcescens catalyze glycoside hydrolysis via a mechanism involving the N-acetyl group of the sugar bound to the)1 subsite. We have studied the degradation of the soluble heteropolymer chitosan, to obtain further insight into catalysis in ChiB and to experimentally assess the proposed processive action of this enzyme. Degradation of chitosans with varying degrees of acetylation was monitored by following the size-distribution of oligomers, and oligomers were isolated and partly sequenced using 1 H-NMR spectroscopy....

12p awards 05-04-2013 55 5   Download

Cytochrome P450 enzymes promote a number of oxidative biotransformations including the hydroxylation of unacti-vated hydrocarbons.

26p awards 05-04-2013 44 7   Download

In haem-regulated phosphodiesterase (PDE) fromEscheri-chia coli(EcDOS), haem is bound to the PAS domain, and the redox state of the haem iron regulates catalysis by the PDEdomain.We generatedmutants ofAsp40, which forms a hydrogen bondwithHis77 (a proximal haemaxial ligand) via twowater molecules, and a salt bridge withArg85 at the protein surface. The redox potential of haem was markedly increased from67 mVvs. the standardhydrogenelectrode in the wild-type enzyme to 95 mV and 114 mV in the Ala and Asn mutants, respectively. ...

6p awards 05-04-2013 42 5   Download

Enzyme catalysis in low water containing organic solvents is finding an increasing number of applications in diverse areas.This review focuses on some aspects which have not been reviewed elsewhere.Different strategies for obtaining higher activity and stability in such media are described.In this context, the damaging role of lyophilization and the means of overcoming such effects are discussed.Ultrasoni-cation and microwave assistance are two emerging approa-ches for enhancing reaction rates in low water media.

9p dell39 03-04-2013 62 4   Download

Mutants of a cobalt-containing nitrile hydratase (NHase, EC 4.2.1.84) fromPseudonocardia thermophilaJCM 3095 involved in substrate binding, catalysis and formation of the active center were constructed, and their characteristics and crystal structures were investigated. As expected fromthe structure of the substrate binding pocket, the wild-type enzyme showed significantly lower KmandKi values for aromatic substrates and inhibitors, respectively, than alipha-ticones.

10p dell39 03-04-2013 25 2   Download

The 3C-like protease of the severe acute respiratory syndrome (SARS) cor-onavirus has a C-terminal extra domain in addition to the chymotrypsin-fold adopted by piconavirus 3C proteases hosting the complete catalytic machinery. Previously we identified the extra domain to be involved in enzyme dimerization which has been considered essential for the catalytic activity.

11p inspiron33 26-03-2013 40 4   Download