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Structure of FAD-bound L-aspartate oxidase: insight into substrate specificity and catalysis.

Bossi RT, Negri A, Tedeschi G, Mattevi A
Biochemistry 41 3018-24 (2002)
Cited: 39 times
EuropePMC logo PMID: 11863440

Abstract

L-Aspartate oxidase (Laspo) catalyzes the conversion of L-Asp to iminoaspartate, the first step in the de novo biosynthesis of NAD(+). This bacterial pathway represents a potential drug target since it is absent in mammals. The Laspo R386L mutant was crystallized in the FAD-bound catalytically competent form and its three-dimensional structure determined at 2.5 A resolution in both the native state and in complex with succinate. Comparison of the R386L holoprotein with the wild-type apoenzyme [Mattevi, A., Tedeschi, G., Bacchella, L., Coda, A., Negri, A., and Ronchi, S. (1999) Structure 7, 745-756] reveals that cofactor incorporation leads to the ordering of two polypeptide segments (residues 44-53 and 104-141) and to a 27 degree rotation of the capping domain. This motion results in the formation of the active site cavity, located at the interface between the capping domain and the FAD-binding domain. The structure of the succinate complex indicates that the cavity surface is decorated by two clusters of H-bond donors that anchor the ligand carboxylates. Moreover, Glu121, which is strictly conserved among Laspo sequences, is positioned to interact with the L-Asp alpha-amino group. The architecture of the active site of the Laspo holoenzyme is remarkably similar to that of respiratory fumarate reductases, providing strong evidence for a common mechanism of catalysis in Laspo and flavoproteins of the succinate dehydrogenase/fumarate reductase family. This implies that Laspo is mechanistically distinct from other flavin-dependent amino acid oxidases, such as the prototypical D-amino acid oxidase.

Articles - 1knp mentioned but not cited (5)

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  2. Biogenesis and Homeostasis of Nicotinamide Adenine Dinucleotide Cofactor. Osterman A. EcoSal Plus 3 (2009)
  3. Mechanistic Characterization of Escherichia coli l-Aspartate Oxidase from Kinetic Isotope Effects. Chow C, Hegde S, Blanchard JS. Biochemistry 56 4044-4052 (2017)
  4. Case study on the evolution of hetero-oligomer interfaces based on the differences in paralogous proteins. Aoto S, Yura K. Biophys Physicobiol 12 103-116 (2015)
  5. Computational Mechanistic Study of l-Aspartate Oxidase by ONIOM Method. Yildiz I. ACS Omega 8 19963-19968 (2023)


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  2. Function and structure of complex II of the respiratory chain. Cecchini G. Annu Rev Biochem 72 77-109 (2003)
  3. A twisted base? The role of arginine in enzyme-catalyzed proton abstractions. Guillén Schlippe YV, Hedstrom L. Arch Biochem Biophys 433 266-278 (2005)
  4. Deflavination and reconstitution of flavoproteins. Hefti MH, Vervoort J, van Berkel WJ. Eur J Biochem 270 4227-4242 (2003)
  5. L-amino acid oxidase as biocatalyst: a dream too far? Pollegioni L, Motta P, Molla G. Appl Microbiol Biotechnol 97 9323-9341 (2013)
  6. L-Amino acid oxidases from microbial sources: types, properties, functions, and applications. Hossain GS, Li J, Shin HD, Du G, Liu L, Chen J. Appl Microbiol Biotechnol 98 1507-1515 (2014)
  7. Catalytic mechanisms of complex II enzymes: a structural perspective. Iverson TM. Biochim Biophys Acta 1827 648-657 (2013)
  8. Distribution in Different Organisms of Amino Acid Oxidases with FAD or a Quinone As Cofactor and Their Role as Antimicrobial Proteins in Marine Bacteria. Campillo-Brocal JC, Lucas-Elío P, Sanchez-Amat A. Mar Drugs 13 7403-7418 (2015)
  9. A mechanistic analysis of enzymatic degradation of organohalogen compounds. Kurihara T. Biosci Biotechnol Biochem 75 189-198 (2011)
  10. An evolving view of complex II-noncanonical complexes, megacomplexes, respiration, signaling, and beyond. Iverson TM, Singh PK, Cecchini G. J Biol Chem 299 104761 (2023)

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  2. Mechanistic investigations of the dehydration reaction of lacticin 481 synthetase using site-directed mutagenesis. You YO, van der Donk WA. Biochemistry 46 5991-6000 (2007)
  3. Solving a Bloody Mess: B-Vitamin Independent Metabolic Convergence among Gammaproteobacterial Obligate Endosymbionts from Blood-Feeding Arthropods and the Leech Haementeria officinalis. Manzano-Marín A, Oceguera-Figueroa A, Latorre A, Jiménez-García LF, Moya A. Genome Biol Evol 7 2871-2884 (2015)
  4. Advances in non-snake venom L-amino acid oxidase. Yu Z, Qiao H. Appl Biochem Biotechnol 167 1-13 (2012)
  5. A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II. Tomasiak TM, Maklashina E, Cecchini G, Iverson TM. J Biol Chem 283 15460-15468 (2008)
  6. Characterization of L-aspartate oxidase and quinolinate synthase from Bacillus subtilis. Marinoni I, Nonnis S, Monteferrante C, Heathcote P, Härtig E, Böttger LH, Trautwein AX, Negri A, Albertini AM, Tedeschi G. FEBS J 275 5090-5107 (2008)
  7. Natural and Synthetic Variants of the Tricarboxylic Acid Cycle in Cyanobacteria: Introduction of the GABA Shunt into Synechococcus sp. PCC 7002. Zhang S, Qian X, Chang S, Dismukes GC, Bryant DA. Front Microbiol 7 1972 (2016)
  8. Crystal structure of the NAD biosynthetic enzyme quinolinate synthase. Sakuraba H, Tsuge H, Yoneda K, Katunuma N, Ohshima T. J Biol Chem 280 26645-26648 (2005)
  9. A soluble NADH-dependent fumarate reductase in the reductive tricarboxylic acid cycle of Hydrogenobacter thermophilus TK-6. Miura A, Kameya M, Arai H, Ishii M, Igarashi Y. J Bacteriol 190 7170-7177 (2008)
  10. High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase. van der Kamp MW, Perruccio F, Mulholland AJ. Chem Commun (Camb) 1874-1876 (2008)
  11. PDB-scale analysis of known and putative ligand-binding sites with structural sketches. Ito J, Tabei Y, Shimizu K, Tomii K, Tsuda K. Proteins 80 747-763 (2012)
  12. Crystal structure of an assembly intermediate of respiratory Complex II. Sharma P, Maklashina E, Cecchini G, Iverson TM. Nat Commun 9 274 (2018)
  13. Chemical rescue and inhibition studies to determine the role of Arg301 in phosphite dehydrogenase. Hung JE, Fogle EJ, Garg N, Chekan JR, Nair SK, van der Donk WA. PLoS One 9 e87134 (2014)
  14. Crystal structure of bacterial succinate:quinone oxidoreductase flavoprotein SdhA in complex with its assembly factor SdhE. Maher MJ, Herath AS, Udagedara SR, Dougan DA, Truscott KN. Proc Natl Acad Sci U S A 115 2982-2987 (2018)
  15. Investigation of the role of Arg301 identified in the X-ray structure of phosphite dehydrogenase. Hung JE, Fogle EJ, Christman HD, Johannes TW, Zhao H, Metcalf WW, van der Donk WA. Biochemistry 51 4254-4262 (2012)
  16. On the catalytic role of the active site residue E121 of E. coli L-aspartate oxidase. Tedeschi G, Nonnis S, Strumbo B, Cruciani G, Carosati E, Negri A. Biochimie 92 1335-1342 (2010)
  17. New crystal forms of the integral membrane Escherichia coli quinol:fumarate reductase suggest that ligands control domain movement. Starbird CA, Tomasiak TM, Singh PK, Yankovskaya V, Maklashina E, Eisenbach M, Cecchini G, Iverson TM. J Struct Biol 202 100-104 (2018)
  18. The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase. Bushnell EA, Erdtman E, Llano J, Eriksson LA, Gauld JW. J Comput Chem 32 822-834 (2011)
  19. Crystal Structures of the Iron-Sulfur Cluster-Dependent Quinolinate Synthase in Complex with Dihydroxyacetone Phosphate, Iminoaspartate Analogues, and Quinolinate. Fenwick MK, Ealick SE. Biochemistry 55 4135-4139 (2016)
  20. Flavin-N5 Covalent Intermediate in a Nonredox Dehalogenation Reaction Catalyzed by an Atypical Flavoenzyme. Dai Y, Kizjakina K, Campbell AC, Korasick DA, Tanner JJ, Sobrado P. Chembiochem 19 53-57 (2018)
  21. Mechanism of Triphosphate Hydrolysis by Human MAT2A at 1.07 Å Resolution. Ghosh A, Niland CN, Cahill SM, Karadkhelkar NM, Schramm VL. J Am Chem Soc 143 18325-18330 (2021)
  22. Production of succinate by engineered strains of Synechocystis PCC 6803 overexpressing phosphoenolpyruvate carboxylase and a glyoxylate shunt. Durall C, Kukil K, Hawkes JA, Albergati A, Lindblad P, Lindberg P. Microb Cell Fact 20 39 (2021)
  23. Molecular and physiological responses in roots of two full-sib poplars uncover mechanisms that contribute to differences in partial submergence tolerance. Peng Y, Zhou Z, Zhang Z, Yu X, Zhang X, Du K. Sci Rep 8 12829 (2018)
  24. Prebiotic Synthesis of Aspartate Using Life's Metabolism as a Guide. Harrison SA, Webb WL, Rammu H, Lane N. Life (Basel) 13 1177 (2023)


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