Hydrogen bonding of flavoprotein: II. Effect of hydrogen bonding at hetero atoms of reduced flavin on its reactivity

doi:10.1016/0304-4165(84)90178-8

Biochimica et Biophysica Acta (BBA) - General Subjects

Volume 802, Issue 2, 28 November 1984, Pages 321-325

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Abstract

The effect of hydrogen bonding at hetero atoms of reduced flavin on its reactivity was studied by ab initio molecular orbital calculations. Among the atoms in the isoalloxazine nucleus of lumiflavin, C(4a) was found to be the most reactive with neutral electrophiles such as molecular oxygen, whereas no reactivity of N(5) can be expected, because of its negative charge. The reactivity of C(4a) is markedly enhanced by hydrogen bonding at N(1) and N(3) in a hydrophobic environment, while it is decreased when hydrogen bonding occurs at all the hetero atoms, as in the case of an aqueous solution of flavin.

References (17)

K. Nishimoto et al.
Biochim. Biophys. Acta
(1978)
T. Spector et al.
J. Biol. Chem.
(1972)
L.M. Schopfer et al.
J. Biol. Chem.
(1980)
P.-S. Song et al.
K. Kawano et al.
Biochemistry
(1978)
Y. Watanabe et al.
R. Ditchfield et al.
J. Chem. Phys.
(1971)
R. Norrestam et al.
Acta Cryst. B
(1969)

There are more references available in the full text version of this article.

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Similarities and differences between cyclobutane pyrimidine dimer photolyase and (6-4) photolyase as revealed by resonance raman spectroscopy: Electron transfer from the FAD cofactor to ultraviolet-damaged DNA
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Citation Excerpt :
This modification of the hydrogen bonding structure of the flavin ring is expected to lead to a significant increase in the redox potential for the semiquinone-hydroquinone couple (53). Furthermore, molecular orbital calculations showed that the weakened hydrogen bond at donor positions (N(3)-H and N(5)-H) would decrease the lowest unoccupied molecular orbital energy (54-56). This would enhance the electron acceptability, increasing the redox potential of flavin.
The cyclobutane pyrimidine dimer (CPD) and (6-4) photoproduct, two major types of DNA damage caused by UV light, are repaired under illumination with near UV-visible light by CPD and (6-4) photolyases, respectively. To understand the mechanism of DNA repair, we examined the resonance Raman spectra of complexes between damaged DNA and the neutral semiquinoid and oxidized forms of (6-4) and CPD photolyases. The marker band for a neutral semiquinoid flavin and band I of the oxidized flavin, which are derived from the vibrations of the benzene ring of FAD, were shifted to lower frequencies upon binding of damaged DNA by CPD photolyase but not by (6-4) photolyase, indicating that CPD interacts with the benzene ring of FAD directly but that the (6-4) photoproduct does not. Bands II and VII of the oxidized flavin and the 1398/1391 cm^-1 bands of the neutral semiquinoid flavin, which may reflect the bending of U-shaped FAD, were altered upon substrate binding, suggesting that CPD and the (6-4) photoproduct interact with the adenine ring of FAD. When substrate was bound, there was an upshifted 1528 cm^-1 band of the neutral semiquinoid flavin in CPD photolyase, indicating a weakened hydrogen bond at N(5)-H of FAD, and band X seemed to be downshifted in (6-4) photolyase, indicating a weakened hydrogen bond at N(3)-H of FAD. These Raman spectra led us to conclude that the two photolyases have different electron transfer mechanisms as well as different hydrogen bonding environments, which account for the higher redox potential of CPD photolyase.
Porcine kidney D-amino acid oxidase: the three-dimensional structure and its catalytic mechanism based on the enzyme-substrate complex model
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The three-dimensional structure of porcine kidney d-amino acid oxidase (DAO), an FAD-dependent oxidase, has been solved by X-ray crystallography. The overall structure is a dimer, subunits of which are correlated by a non-crystallographic two-fold axis. Each subunit comprises two domains, ‘αβ domain’ and ‘pseudo-barrel domain’. The coenzyme FAD is in an elongated conformation and is bound at the N-terminal βαβ dinucleotide binding motif. The active site is located in the boundary region between the two domains. The crystal structure of DAO in complex with a substrate analog, o-aminobenzoate, was also solved and is used for modeling the DAO-d-leucine complex, i.e. Michaelis complex, by means of molecular mechanics simulation. The Michaelis-complex model provided structural information leading to two alternative hypothetical mechanisms for the reductive half-reaction of DAO. These two hypotheses characterize themselves by electron transfer from the lone-pair orbital of the substrate amino nitrogen to flavin C(4a) and by proton transfer from the substrate α-position to flavin N(5) which acts as a catalytic base.
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It seems widely accepted that the reductive half reaction of d-amino acid oxidase is initiated by the carbanion which is generated as the result of the α-proton abstraction from the substrate d-amino acid by a protein nucleophile. However, this process is energetically unfavorable even in the enzyme-substrate complex irrespective of how short the lifetime of the carbanion might be. To circumvent this dilemma the authors have put forward an alternative mechanism, according to which the α-proton abstraction by the protein nucleophile is coupled in a concerted manner with the electron transfer from the amino nitrogen of the substrate to the oxidized flavin without intermediary generation of the carbanion as a discrete entity. The present review describes the background and the rationales for the concerted mechanism with specific emphasis on the flavin-substrate (intermediate) chargetransfer interactions.
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Crystals of the flavin-containing enzyme p-hydroxybenzoate hydroxylase (PHBHase) complexed with its reaction product were investigated in order to obtain insight into the catalytic cycle of this enzyme involving two substrates and two cofactors. PHBHase was crystallized initially with its substrate, p-hydroxybenzoate and the substrate was then converted into the product 3,4-dihydroxybenzoate by allowing the catalytic reaction to proceed in the crystals. In addition, crystals were soaked in mother liquor containing a high concentration of this product.
Data up to 2.3 Å (1 Å = 0.1 nm) were collected by the oscillation method and the structure of the enzyme product complex was refined by alternate restrained least-squares procedures and model building by computer graphics techniques. A total of 273 solvent molecules could be located, four of them being presumably sulfate ions. The R-factor for 14,339 reflections between 6.0 Å and 2.3 Å is 19.3%.
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^☆: The first paper in this series is Ref. 3.

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Biochimica et Biophysica Acta (BBA) - General Subjects

Hydrogen bonding of flavoprotein: II. Effect of hydrogen bonding at hetero atoms of reduced flavin on its reactivity☆

Abstract

Biochim. Biophys. Acta

J. Biol. Chem.

J. Biol. Chem.

Biochemistry

J. Chem. Phys.

Acta Cryst. B

Similarities and differences between cyclobutane pyrimidine dimer photolyase and (6-4) photolyase as revealed by resonance raman spectroscopy: Electron transfer from the FAD cofactor to ultraviolet-damaged DNA

Porcine kidney D-amino acid oxidase: the three-dimensional structure and its catalytic mechanism based on the enzyme-substrate complex model

Commentary on "Crystallization of Michaelis complex of d-amino acid oxidase' by K. Yagi and T. Ozawa Biochim. Biophys. Acta 60 (1962) 200-201

The reaction mechanism of d-amino acid oxidase: Concerted or not concerted?

Crystal structure of p-hydroxybenzoate hydroxylase complexed with its reaction product 3,4-dihydroxybenzoate

Coupling of NAD(P)H:FMN-oxidoreductase and luciferase from luminous bacteria in a viscous medium: Finding the weakest link in the chain