Inactivation of Mandelate Racemase by 3-Hydroxypyruvate Reveals a Potential Mechanistic Link between Enzyme Superfamilies

Mandelate racemase (MR), a member of the enolase superfamily, catalyzes the Mg2+-dependent interconversion of the enantiomers of mandelate. Several α-keto acids are modest competitive inhibitors of MR [e.g., mesoxalate (Ki = 1.8 ± 0.3 mM) and 3-fluoropyruvate (Ki = 1.3 ± 0.1 mM)], but, surprisingly, 3-hydroxypyruvate (3-HP) is an irreversible, time-dependent inhibitor (kinact/KI = 83 ± 8 M–1 s–1). Protection from inactivation by the competitive inhibitor benzohydroxamate, trypsinolysis and electrospray ionization tandem mass spectrometry analyses, and X-ray crystallographic studies reveal that 3-HP undergoes Schiff-base formation with Lys 166 at the active site, followed by formation of an aldehyde/enol(ate) adduct. Such a reaction is unprecedented in the enolase superfamily and may be a relic of an activity possessed by a promiscuous progenitor enzyme. The ability of MR to form and deprotonate a Schiff-base intermediate furnishes a previously unrecognized mechanistic link to other α/β-barrel enzymes utilizing Schiff-base chemistry and is in accord with the sequence- and structure-based hypothesis that members of the metal-dependent enolase superfamily and the Schiff-base-forming N-acetylneuraminate lyase superfamily and aldolases share a common ancestor

Generalized Morse Wavelets as a Superfamily of Analytic Wavelets

The generalized Morse wavelets are shown to constitute a superfamily that essentially encompasses all other commonly used analytic wavelets, subsuming eight apparently distinct types of analysis filters into a single common form. This superfamily of analytic wavelets provides a framework for systematically investigating wavelet suitability for various applications. In addition to a parameter controlling the time-domain duration or Fourier-domain bandwidth, the wavelet {\em shape} with fixed bandwidth may be modified by varying a second parameter, called $\gamma$. For integer values of $\gamma$, the most symmetric, most nearly Gaussian, and generally most time-frequency concentrated member of the superfamily is found to occur for $\gamma=3$. These wavelets, known as "Airy wavelets," capture the essential idea of popular Morlet wavelet, while avoiding its deficiencies. They may be recommended as an ideal starting point for general purpose use

Experiment Pamir-2. Fianit: A giant super-family with halo (Epsilon sub 0 at approximately 10(17) eV)

A superfamily with halo of extremely high energy named Fianit was recorded in X-ray emulsion chamber (XEC) at the Pamirs (atmospheric depth 600 g/sq.cm.). Detailed description of the superfamily and results of its analysis are presented

Sequence and function of the two P domain potassium channels: implications of an emerging superfamily.

A new superfamily of K+ channels has emerged in the past 2 years. Notable for possessing two pore-forming P domains in each subunit, members of the superfamily have been recognized through phylogeny from micro-organisms to humans. Four subfamilies of two P domain channels have been isolated thus far; among these are the first cloned examples of outward rectifier and open rectifier (or leak) K+ channels. The two P domain K+ channels offer a new perspective from which to glimpse the molecular basis for function and dysfunction of K+-selective ion channels

Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily.

Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination of tools that include large-scale phylogenetic reconstruction to determine the sequence, structural, and functional relationships of the functionally diverse flavin mononucleotide-dependent nitroreductase (NTR) superfamily (>24,000 sequences from all domains of life, 54 structures, and >10 enzymatic functions). Our results suggest an evolutionary model in which contemporary subgroups of the superfamily have diverged in a radial manner from a minimal flavin-binding scaffold. We identified the structural design principle for this divergence: Insertions at key positions in the minimal scaffold that, combined with the fixation of key residues, have led to functional specialization. These results will aid future efforts to delineate the emergence of functional diversity in enzyme superfamilies, provide clues for functional inference for superfamily members of unknown function, and facilitate rational redesign of the NTR scaffold

Convergent dynamics in the protease enzymatic superfamily

Proteases regulate various aspects of the life cycle in all organisms by cleaving specific peptide bonds. Their action is so central for biochemical processes that at least 2% of any known genome encodes for proteolytic enzymes. Here we show that selected proteases pairs, despite differences in oligomeric state, catalytic residues and fold, share a common structural organization of functionally relevant regions which are further shown to undergo similar concerted movements. The structural and dynamical similarities found pervasively across evolutionarily distant clans point to common mechanisms for peptide hydrolysis.Comment: 13 pages, 6 figure