scholarly journals The effect of active-site isoleucine to alanine mutation on the DHFR catalyzed hydride-transfer

2010 ◽  
Vol 46 (47) ◽  
pp. 8974 ◽  
Author(s):  
Vanja Stojković ◽  
Laura L. Perissinotti ◽  
Jeeyeon Lee ◽  
Stephen J. Benkovic ◽  
Amnon Kohen
Keyword(s):  
Active Site ◽  
Hydride Transfer

scholarly journals Crystal Structure of the FAD-Containing Ferredoxin-NADP+Reductase from the Plant PathogenXanthomonas axonopodispv. citri

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
María Laura Tondo ◽  
Ramon Hurtado-Guerrero ◽  
Eduardo A. Ceccarelli ◽  
Milagros Medina ◽  
Elena G. Orellano ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Transfer Process ◽  
Plant Pathogen ◽  
Active Site ◽  
Functional Divergence ◽  
Hydride Transfer ◽  
Citrus Canker ◽  
Xanthomonas Axonopodis ◽  
C Terminus

We have solved the structure of ferredoxin-NADP(H) reductase, FPR, from the plant pathogenXanthomonas axonopodispv. citri, responsible for citrus canker, at a resolution of 1.5 Å. This structure reveals differences in the mobility of specific loops when compared to other FPRs, probably unrelated to the hydride transfer process, which contributes to explaining the structural and functional divergence between the subclass I FPRs. Interactions of the C-terminus of the enzyme with the phosphoadenosine of the cofactor FAD limit its mobility, thus affecting the entrance of nicotinamide into the active site. This structure opens the possibility of rationally designing drugs against theX. axonopodispv. citri phytopathogen.

scholarly journals Structure and function of yeast alcohol dehydrogenase

2000 ◽  
Vol 65 (4) ◽  
pp. 207-227 ◽  
Author(s):  
Svetlana Trivic ◽  
Vladimir Leskovac
Keyword(s):  
Alcohol Dehydrogenase ◽  
Substrate Specificity ◽  
Primary Structure ◽  
Active Site ◽  
Hydride Transfer ◽  
Kinetic Mechanism ◽  
Structure And Function ◽  
Chemical Mechanism ◽  
And Function ◽  
Font Color

1. Introduction 2. Isoenzymes of YADH 3. Substrate specificity 4. Kinetic mechanism 5. Primary structure 6. The active site 7. Mutations in the yeast enzyme 8. Chemical mechanism 9. Binding of coenzymes 10. Hydride transfer <br><br><font color="red"><b> This article has been corrected. Link to the correction <u><a href="http://dx.doi.org/10.2298/JSC0008609E">10.2298/JSC0008609E</a><u></b></font>

scholarly journals The influence of active site conformations on the hydride transfer step of the thymidylate synthase reaction mechanism

2015 ◽  
Vol 17 (46) ◽  
pp. 30793-30804 ◽  
Author(s):  
Katarzyna Świderek ◽  
Amnon Kohen ◽  
Vicent Moliner
Keyword(s):  
Reaction Mechanism ◽  
Thymidylate Synthase ◽  
Active Site ◽  
Hydride Transfer ◽  
Md Simulations ◽  
Concerted Mechanism ◽  
X Ray ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Rate Limiting

QM/MM MD simulations from different X-ray structures support the concerted mechanism character in the rate limiting step of thymidylate synthase catalysis.

scholarly journals Mg2+ Binds to the Surface of Thymidylate Synthase and Affects Hydride Transfer at the Interior Active Site

2013 ◽  
Vol 135 (20) ◽  
pp. 7583-7592 ◽  
Author(s):  
Zhen Wang ◽  
Paul J. Sapienza ◽  
Thelma Abeysinghe ◽  
Calvin Luzum ◽  
Andrew L. Lee ◽  
...  
Keyword(s):  
Thymidylate Synthase ◽  
Active Site ◽  
Hydride Transfer

scholarly journals Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions

2010 ◽  
Vol 66 (6) ◽  
pp. 673-684 ◽  
Author(s):  
Radhika Malik ◽  
Ronald E. Viola
Keyword(s):  
Active Site ◽  
Metal Ion ◽  
Substrate Binding ◽  
Hydride Transfer ◽  
Divalent Metal ◽  
Ammonium Ion ◽  
Hydroxyl Group ◽  
Metal Ion Binding ◽  
Cofactor Binding ◽  
Divalent Metal Ion

The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 Å resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg2+and NADH. This TDH structure fromPseudomonas putidahas a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.

scholarly journals Kinetic and chemical characterization of aldehyde oxidation by fungal aryl-alcohol oxidase

2010 ◽  
Vol 425 (3) ◽  
pp. 585-593 ◽  
Author(s):  
Patricia Ferreira ◽  
Aitor Hernández-Ortega ◽  
Beatriz Herguedas ◽  
Jorge Rencoret ◽  
Ana Gutiérrez ◽  
...  
Keyword(s):  
Active Site ◽  
Chemical Characterization ◽  
Alcohol Oxidase ◽  
Hydride Transfer ◽  
Aldehyde Oxidase ◽  
Site Directed Mutagenesis ◽  
Lignin Biodegradation ◽  
Aryl Aldehyde ◽  
Aldehyde Oxidation ◽  
Solvent Isotope

Fungal AAO (aryl-alcohol oxidase) provides H2O2 for lignin biodegradation. AAO is active on benzyl alcohols that are oxidized to aldehydes. However, during oxidation of some alcohols, AAO forms more than a stoichiometric number of H2O2 molecules with respect to the amount of aldehyde detected due to a double reaction that involves aryl-aldehyde oxidase activity. The latter reaction was investigated using different benzylic aldehydes, whose oxidation to acids was demonstrated by GC-MS. The steady- and presteady state kinetic constants, together with the chromatographic results, revealed that the presence of substrate electron-withdrawing or electron-donating substituents had a strong influence on activity; the highest activity was with p-nitrobenzaldehyde and halogenated aldehydes and the lowest with methoxylated aldehydes. Moreover, activity was correlated to the aldehyde hydration rates estimated by 1H-NMR. These findings, together with the absence in the AAO active site of a residue able to drive oxidation via an aldehyde thiohemiacetal, suggested that oxidation mainly proceeds via the gem-diol species. The reaction mechanism (with a solvent isotope effect, 2H2Okred, of approx. 1.5) would be analogous to that described for alcohols, the reductive half-reaction involving concerted hydride transfer from the α-carbon and proton abstraction from one of the gem-diol hydroxy groups by a base. The existence of two steps of opposite polar requirements (hydration and hydride transfer) explains some aspects of aldehyde oxidation by AAO. Site-directed mutagenesis identified two histidine residues strongly involved in gem-diol oxidation and, unexpectedly, suggested that an active-site tyrosine residue could facilitate the oxidation of some aldehydes that show no detectable hydration. Double alcohol and aldehyde oxidase activities of AAO would contribute to H2O2 supply by the enzyme.

scholarly journals Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase

ACS Catalysis ◽  
2020 ◽  
Vol 10 (19) ◽  
pp. 11253-11267
Author(s):  
Anil R. Mhashal ◽  
Adrian Romero-Rivera ◽  
Lisa S. Mydy ◽  
Judith R. Cristobal ◽  
Andrew M. Gulick ◽  
...  
Keyword(s):  
Active Site ◽  
Hydride Transfer ◽  
Side Chains ◽  
Flexible Loop ◽  
Glycerol 3 Phosphate Dehydrogenase
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