The structure of a nativel-amino acid oxidase, the major component of the Vipera ammodytes ammodytes venomic, reveals dynamic active site and quaternary structure stabilization by divalent ions

2011 ◽  
Vol 7 (2) ◽  
pp. 379-384 ◽  
Author(s):  
Dessislava Georgieva ◽  
Mario Murakami ◽  
Markus Perband ◽  
Raghuvir Arni ◽  
Christian Betzel
Keyword(s):  
Amino Acid ◽  
Active Site ◽  
Quaternary Structure ◽  
Acid Oxidase ◽  
Divalent Ions ◽  
Amino Acid Oxidase ◽  
Structure Stabilization ◽  
Vipera Ammodytes

P219L substitution in human D-amino acid oxidase impacts the ligand binding and catalytic efficiency

2020 ◽  
Vol 168 (5) ◽  
pp. 557-567
Author(s):  
Wanitcha Rachadech ◽  
Yusuke Kato ◽  
Rabab M Abou El-Magd ◽  
Yuji Shishido ◽  
Soo Hyeon Kim ◽  
...  
Keyword(s):  
Amino Acid ◽  
Conformational Changes ◽  
Active Site ◽  
Structural Changes ◽  
Catalytic Efficiency ◽  
Acid Oxidase ◽  
Wild Type ◽  
Amino Acid Oxidase ◽  
Adenine Ring ◽  
The Impact

Abstract Human D-amino acid oxidase (DAO) is a flavoenzyme that is implicated in neurodegenerative diseases. We investigated the impact of replacement of proline with leucine at Position 219 (P219L) in the active site lid of human DAO on the structural and enzymatic properties, because porcine DAO contains leucine at the corresponding position. The turnover numbers (kcat) of P219L were unchanged, but its Km values decreased compared with wild-type, leading to an increase in the catalytic efficiency (kcat/Km). Moreover, benzoate inhibits P219L with lower Ki value (0.7–0.9 µM) compared with wild-type (1.2–2.0 µM). Crystal structure of P219L in complex with flavin adenine dinucleotide (FAD) and benzoate at 2.25 Å resolution displayed conformational changes of the active site and lid. The distances between the H-bond-forming atoms of arginine 283 and benzoate and the relative position between the aromatic rings of tyrosine 224 and benzoate were changed in the P219L complex. Taken together, the P219L substitution leads to an increase in the catalytic efficiency and binding affinity for substrates/inhibitors due to these structural changes. Furthermore, an acetic acid was located near the adenine ring of FAD in the P219L complex. This study provides new insights into the structure–function relationship of human DAO.

Engineering the Substrate Specificity of Porcine Kidney d-Amino Acid Oxidase by Mutagenesis of the “Active-Site Lid”

2006 ◽  
Vol 139 (5) ◽  
pp. 873-879 ◽  
Author(s):  
Chiaki Setoyama ◽  
Yasuzo Nishina ◽  
Hisashi Mizutani ◽  
Ikuko Miyahara ◽  
Ken Hirotsu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Substrate Specificity ◽  
Active Site ◽  
Acid Oxidase ◽  
Porcine Kidney ◽  
Amino Acid Oxidase

scholarly journals Synthesis and Biochemical Evaluation of Lid-Open D-Amino Acid Oxidase Inhibitors

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 290
Author(s):  
Bence Szilágyi ◽  
Csilla Hargitai ◽  
Ádám A. Kelemen ◽  
Anita Rácz ◽  
György G. Ferenczy ◽  
...  
Keyword(s):  
Amino Acid ◽  
Physicochemical Properties ◽  
Active Site ◽  
Binding Pocket ◽  
Acid Oxidase ◽  
Amino Acid Oxidase ◽  
New Class ◽  
Biochemical Evaluation ◽  
Low Sensitivity ◽  
Adme Profile

Most of the known inhibitors of D-amino acid oxidase (DAAO) are small polar molecules recognized by the active site of the enzyme. More recently a new class of DAAO inhibitors has been disclosed that interacts with loop 218−224 at the top of the binding pocket. These compounds have a significantly larger size and more beneficial physicochemical properties than most reported DAAO inhibitors, however, their structure-activity relationship is poorly explored. Here we report the synthesis and evaluation of this type of DAAO inhibitors that open the lid over the active site of DAAO. In order to collect relevant SAR data we varied two distinct parts of the inhibitors. A systematic variation of the pendant aromatic substituents according to the Topliss scheme resulted in DAAO inhibitors with low nanomolar activity. The activity showed low sensitivity to the substituents investigated. The variation of the linker connecting the pendant aromatic moiety and the acidic headgroup revealed that the interactions of the linker with the enzyme were crucial for achieving significant inhibitory activity. Structures and activities were analyzed based on available X-ray structures of the complexes. Our findings might support the design of drug-like DAAO inhibitors with advantageous physicochemical properties and ADME profile.

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 Mechanistic insights into the loss-of-function mechanisms of rare human D-amino acid oxidase variants implicated in amyotrophic lateral sclerosis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Aditya K. Padhi ◽  
Kam Y. J. Zhang
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Amino Acid ◽  
Active Site ◽  
Functional Characterization ◽  
Acid Oxidase ◽  
Missense Mutations ◽  
Salt Bridges ◽  
Amino Acid Oxidase ◽  
Structural Dynamic ◽  
Lateral Sclerosis

Abstract Impaired enzymatic activity in D-amino acid oxidase (DAAO) caused by missense mutations has been shown to trigger amyotrophic lateral sclerosis (ALS) through an abnormal accumulation of D-serine in the spinal cord. While loss of enzymatic functions of certain ALS-causing DAAO variants have been studied before, a detailed understanding of structure-dynamics-function relationship of the rare DAAO variants has not been investigated hitherto. To address this, we carried out a comprehensive study of all the reported rare DAAO variants. By employing a spectrum of bioinformatics analyses along with extensive structural dynamics simulations, we show that certain rare variants disrupted key interactions with the active site and decreased the conformational flexibility of active site loop comprising residues 216–228, which is essential for substrate binding and product release. Moreover, these variants lost crucial interactions with the cofactor flavin-adenine-dinucleotide, resulting in weaker binding affinity. A detailed inspection revealed that these variants exhibited such characteristics due to the abrogation of specific salt bridges. Taken together, our study provides a gateway into the structural-dynamic features of the rare DAAO variants and highlights the importance of informatics-based integrated analyses in the screening and prioritization of variants a priori to the clinical-functional characterization.

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