scholarly journals Structures of aspartate aminotransferases fromTrypanosoma brucei,Leishmania majorandGiardia lamblia

2015 ◽  
Vol 71 (5) ◽  
pp. 566-571 ◽  
Author(s):  
Jan Abendroth ◽  
Ryan Choi ◽  
Abigail Wall ◽  
Matthew C. Clifton ◽  
Christine M. Lukacs ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Schiff Base ◽  
Trypanosoma Brucei ◽  
Structural Genomics ◽  
Active Site ◽  
Pyridoxal Phosphate ◽  
Inhibitor Design

The structures of three aspartate aminotransferases (AATs) from eukaryotic pathogens were solved within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). Both the open and closed conformations of AAT were observed. Pyridoxal phosphate was bound to the active siteviaa Schiff base to a conserved lysine. An active-site mutant showed thatTrypanosoma bruceiAAT still binds pyridoxal phosphate even in the absence of the tethering lysine. The structures highlight the challenges for the structure-based design of inhibitors targeting the active site, while showing options for inhibitor design targeting the N-terminal arm.

scholarly journals The mechanism of action of serine transhydroxymethylase

1970 ◽  
Vol 116 (2) ◽  
pp. 277-286 ◽  
Author(s):  
P. M. Jordan ◽  
M. Akhtar
Keyword(s):  
Schiff Base ◽  
Amino Acid ◽  
Hydrogen Atom ◽  
Mechanism Of Action ◽  
Active Site ◽  
Enzyme Preparation ◽  
Pyridoxal Phosphate ◽  
Acid Oxidase ◽  
Amino Acid Oxidase

1. The preparation of stereospecifically tritiated glycines and the determination of their absolute configurations by the use of d-amino acid oxidase are described. 2. The reaction catalysed by serine transhydroxymethylase, which results in the conversion of glycine into serine, has been separated into at least four partial reactions. It is suggested that the first event in this conversion is the formation of a Schiff base intermediate of glycine and pyridoxal phosphate. The next important step involves the removal of the 2S-hydrogen atom of glycine to give a carbanion intermediate. Experiments pertinent to the mechanism of conversion of this carbanion intermediate into serine are described. 3. The enzyme preparation catalysing the conversion of glycine into serine also participates in the conversion of glycine into threonine and allothreonine. In both these conversions, glycine → serine and glycine → threonine, the 2S-hydrogen atom of glycine is eliminated and the 2R-hydrogen atom of glycine is retained. 4. In the light of these experiments the mechanism of action of serine transhydroxymethylase is discussed. It is suggested that methylenetetrahydrofolate is the carrier of formaldehyde, from which formaldehyde may be liberated at the active site of the enzyme, thus allowing the overall reaction to take place.

scholarly journals Structures of a histidine triad family protein fromEntamoeba histolyticabound to sulfate, AMP and GMP

2015 ◽  
Vol 71 (5) ◽  
pp. 572-576 ◽  
Author(s):  
Donald D. Lorimer ◽  
Ryan Choi ◽  
Ariel Abramov ◽  
Stephen Nakazawa Hewitt ◽  
Anna S. Gardberg ◽  
...  
Keyword(s):  
Infectious Disease ◽  
High Resolution ◽  
Entamoeba Histolytica ◽  
Causative Agent ◽  
Structural Genomics ◽  
Active Site ◽  
Amoebic Dysentery ◽  
Family Protein

Three structures of the histidine triad family protein fromEntamoeba histolytica, the causative agent of amoebic dysentery, were solved at high resolution within the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The structures have sulfate (PDB entry 3oj7), AMP (PDB entry 3omf) or GMP (PDB entry 3oxk) bound in the active site, with sulfate occupying the same space as the α-phosphate of the two nucleotides. The Cαbackbones of the three structures are nearly superimposable, with pairwise r.m.s.d.s ranging from 0.06 to 0.13 Å.

scholarly journals Active-site-directed inactivation of wheat-germ aspartate transcarbamoylase by pyridoxal 5′-phosphate

1987 ◽  
Vol 248 (2) ◽  
pp. 403-408 ◽  
Author(s):  
S C J Cole ◽  
R J Yon
Keyword(s):  
Schiff Base ◽  
Active Site ◽  
Wheat Germ ◽  
Pyridoxal Phosphate ◽  
Order Rate Constant ◽  
Competitive Inhibitor ◽  
Aspartate Transcarbamoylase ◽  
Carbamoyl Phosphate ◽  
Active Centre ◽  
First Order

Treatment of 1 microM wheat-germ aspartate transcarbamoylase with 1 mM-pyridoxal 5′-phosphate caused a rapid loss of activity, concomitant with the formation of a Schiff base. Complete loss of activity occurred within 10 min when the Schiff base was reduced with a 100-fold excess of NaBH4. Concomitantly, one amino group per chain was modified. No further residues were modified in the ensuing 30 min. The kinetics of inactivation were examined under conditions where the Schiff base was reduced before assay. Inactivation was apparently first-order. The pseudo-first-order rate constant, kapp., showed a hyperbolic dependence upon the concentration of pyridoxal 5′-phosphate, suggesting that the enzyme first formed a non-covalent complex with the reagent, modification of a lysine then proceeding within this complex. Inactivation of the enzyme by pyridoxal was 20 times slower than that by pyridoxal 5′-phosphate, indicating that the phosphate group was important in forming the initial complex. Partial protection against pyridoxal phosphate was provided by the leading substrate, carbamoyl phosphate, and nearly complete protection was provided by the bisubstrate analogue, N-phosphonoacetyl-L-aspartate, and the ligand-pair carbamoyl phosphate plus succinate. Steady-state kinetic studies, under conditions that minimized inactivation, showed that pyridoxal 5′-phosphate was also a competitive inhibitor with respect to the leading substrate, carbamoyl phosphate. Pyridoxal 5′-phosphate therefore appears to be an active-site-directed reagent. A sample of the enzyme containing one reduced pyridoxyl group per chain was digested with trypsin, and the labelled peptide was isolated and shown to contain a single pyridoxyl-lysine residue. Partial sequencing around the labelled lysine showed little homology with the sequence surrounding lysine-84, an active-centre residue of the catalytic subunit of aspartate transcarbamoylase from Escherichia coli, whose reaction with pyridoxal 5′-phosphate shows many similarities to the results described in the present paper. Arguably the reactive lysine is conserved between the two enzymes whereas the residues immediately surrounding the lysine are not. The same conclusion has been drawn in a comparison of reactive histidine residues in the two enzymes [Cole & Yon (1986) Biochemistry 25, 7168-7174].

scholarly journals Crystal structures of human CtBP in complex with substrate MTOB reveal active site features useful for inhibitor design

FEBS Letters ◽  
2014 ◽  
Vol 588 (9) ◽  
pp. 1743-1748 ◽  
Author(s):  
Brendan J. Hilbert ◽  
Steven R. Grossman ◽  
Celia A. Schiffer ◽  
William E. Royer
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
Inhibitor Design

scholarly journals Structure-Based Dissection of the Active Site Chemistry of Leukotriene A4 Hydrolase: Implications for M1 Aminopeptidases and Inhibitor Design

2008 ◽  
Vol 15 (9) ◽  
pp. 920-929 ◽  
Author(s):  
Fredrik Tholander ◽  
Ayumo Muroya ◽  
Bernard-Pierre Roques ◽  
Marie-Claude Fournié-Zaluski ◽  
Marjolein M.G.M. Thunnissen ◽  
...  
Keyword(s):  
Active Site ◽  
Inhibitor Design ◽  
Leukotriene A4 Hydrolase ◽  
Leukotriene A4

A shared mechanistic pathway for pyridoxal phosphate–dependent arginine oxidases

2021 ◽  
Vol 118 (40) ◽  
pp. e2012591118
Author(s):  
Elesha R. Hoffarth ◽  
Kersti Caddell Haatveit ◽  
Eugene Kuatsjah ◽  
Gregory A. MacNeil ◽  
Simran Saroya ◽  
...  
Keyword(s):  
Active Site ◽  
Evolutionary History ◽  
Pyridoxal Phosphate ◽  
Computational Studies ◽  
Single Electron Transfer ◽  
Oxidation Reactions ◽  
Unified Framework ◽  
Precise Positioning ◽  
X Ray ◽  
Mechanistic Pathway

The mechanism by which molecular oxygen is activated by the organic cofactor pyridoxal phosphate (PLP) for oxidation reactions remains poorly understood. Recent work has identified arginine oxidases that catalyze desaturation or hydroxylation reactions. Here, we investigate a desaturase from the Pseudoalteromonas luteoviolacea indolmycin pathway. Our work, combining X-ray crystallographic, biochemical, spectroscopic, and computational studies, supports a shared mechanism with arginine hydroxylases, involving two rounds of single-electron transfer to oxygen and superoxide rebound at the 4′ carbon of the PLP cofactor. The precise positioning of a water molecule in the active site is proposed to control the final reaction outcome. This proposed mechanism provides a unified framework to understand how oxygen can be activated by PLP-dependent enzymes for oxidation of arginine and elucidates a shared mechanistic pathway and intertwined evolutionary history for arginine desaturases and hydroxylases.

scholarly journals Acrolein, an irreversible active-site-directed inhibitor of deoxyribose 5-phosphate aldolase?

1976 ◽  
Vol 153 (2) ◽  
pp. 495-497 ◽  
Author(s):  
D C Wilton
Keyword(s):  
Schiff Base ◽  
Rate Constant ◽  
Active Site ◽  
Order Rate Constant ◽  
Lysine Residue ◽  
Prolonged Incubation ◽  
Enzyme Active Site ◽  
First Order ◽  
Substrate Analogue ◽  
Pseudo First Order

The enzyme deoxyribose 5-phosphate aldolase was irreversibly inactivated by the substrate analogue acrolein with a pseudo-first-order rate constant of 0.324 min-1 and a Ki (apparent) of 2.7 × 10(-4) m. No inactivation was observed after prolonged incubation with the epoxide analogues glycidol phosphate and glycidaldehyde. It is suggested that the acrolein is first activated by forming a Schiff base with the enzyme active-site lysine residue and it is the activated inhibitor that reacts with a suitable-active-site nucleophile.

scholarly journals Fragment Screening of Infectious Disease Targets in a Structural Genomics Environment

2011 ◽  
pp. 533-556 ◽  
Author(s):  
Darren W. Begley ◽  
Douglas R. Davies ◽  
Robert C. Hartley ◽  
Thomas E. Edwards ◽  
Bart L. Staker ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Structural Genomics ◽  
Fragment Screening
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