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Crystal structures of the carboxyl terminal domain of rat 10-formyltetrahydrofolate dehydrogenase: implications for the catalytic mechanism of aldehyde dehydrogenases.

Tsybovsky Y, Donato H, Krupenko NI, Davies C, Krupenko SA
Biochemistry 46 2917-29 (2007)
Related entries: 2o2p, 2o2q

Cited: 46 times
EuropePMC logo PMID: 17302434

Abstract

10-Formyltetrahydrofolate dehydrogenase (FDH) catalyzes an NADP+-dependent dehydrogenase reaction resulting in conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. This reaction is a result of the concerted action of two catalytic domains of FDH, the amino-terminal hydrolase domain and the carboxyl-terminal aldehyde dehydrogenase domain. In addition to participation in the overall FDH mechanism, the C-terminal domain is capable of NADP+-dependent oxidation of short chain aldehydes to their corresponding acids. We have determined the crystal structure of the C-terminal domain of FDH and its complexes with oxidized and reduced forms of NADP. Compared to other members of the ALDH family, FDH demonstrates a new mode of binding of the 2'-phosphate group of NADP via a water-mediated contact with Gln600 that may contribute to the specificity of the enzyme for NADP over NAD. The structures also suggest how Glu673 can act as a general base in both acylation and deacylation steps of the reaction. In the apo structure, the general base Glu673 is positioned optimally for proton abstraction from the sulfur atom of Cys707. Upon binding of NADP+, the side chain of Glu673 is displaced from the active site by the nicotinamide ring and contacts a chain of highly ordered water molecules that may represent a pathway for translocation of the abstracted proton from Glu673 to the solvent. When reduced, the nicotinamide ring of NADP is displaced from the active site, restoring the contact between Cys707 and Glu673 and allowing the latter to activate the hydrolytic water molecule in deacylation.

Articles - 2o2r mentioned but not cited (2)

  1. Modeling of interactions between functional domains of ALDH1L1. Horita DA, Krupenko SA. Chem Biol Interact 276 23-30 (2017)
  2. NADP-Dependent Aldehyde Dehydrogenase from Archaeon Pyrobaculum sp.1860: Structural and Functional Features. Bezsudnova EY, Petrova TE, Artemova NV, Boyko KM, Shabalin IG, Rakitina TV, Polyakov KM, Popov VO. Archaea 2016 9127857 (2016)


Reviews citing this publication (6)

  1. Non-P450 aldehyde oxidizing enzymes: the aldehyde dehydrogenase superfamily. Marchitti SA, Brocker C, Stagos D, Vasiliou V. Expert Opin Drug Metab Toxicol 4 697-720 (2008)
  2. FDH: an aldehyde dehydrogenase fusion enzyme in folate metabolism. Krupenko SA. Chem Biol Interact 178 84-93 (2009)
  3. Kinetic and structural features of betaine aldehyde dehydrogenases: mechanistic and regulatory implications. Muñoz-Clares RA, Díaz-Sánchez AG, González-Segura L, Montiel C. Arch Biochem Biophys 493 71-81 (2010)
  4. Loss of ALDH1L1 folate enzyme confers a selective metabolic advantage for tumor progression. Krupenko SA, Krupenko NI. Chem Biol Interact 302 149-155 (2019)
  5. The Role of Single-Nucleotide Polymorphisms in the Function of Candidate Tumor Suppressor ALDH1L1. Krupenko SA, Horita DA. Front Genet 10 1013 (2019)
  6. Folate Metabolism in Hepatocellular Carcinoma. What Do We Know So Far? Quevedo-Ocampo J, Escobedo-Calvario A, Souza-Arroyo V, Miranda-Labra RU, Bucio-Ortiz L, Gutiérrez-Ruiz MC, Chávez-Rodríguez L, Gomez-Quiroz LE. Technol Cancer Res Treat 21 15330338221144446 (2022)

Articles citing this publication (38)

  1. ALDH1L2 is the mitochondrial homolog of 10-formyltetrahydrofolate dehydrogenase. Krupenko NI, Dubard ME, Strickland KC, Moxley KM, Oleinik NV, Krupenko SA. J Biol Chem 285 23056-23063 (2010)
  2. The crystal structure of a ternary complex of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa Provides new insight into the reaction mechanism and shows a novel binding mode of the 2'-phosphate of NADP+ and a novel cation binding site. González-Segura L, Rudiño-Piñera E, Muñoz-Clares RA, Horjales E. J Mol Biol 385 542-557 (2009)
  3. Development of a high-throughput in vitro assay to identify selective inhibitors for human ALDH1A1. Morgan CA, Hurley TD. Chem Biol Interact 234 29-37 (2015)
  4. Proteomic analysis of fructose-induced fatty liver in hamsters. Zhang L, Perdomo G, Kim DH, Qu S, Ringquist S, Trucco M, Dong HH. Metabolism 57 1115-1124 (2008)
  5. Conserved catalytic residues of the ALDH1L1 aldehyde dehydrogenase domain control binding and discharging of the coenzyme. Tsybovsky Y, Krupenko SA. J Biol Chem 286 23357-23367 (2011)
  6. Enzymatic properties of ALDH1L2, a mitochondrial 10-formyltetrahydrofolate dehydrogenase. Strickland KC, Krupenko NI, Dubard ME, Hu CJ, Tsybovsky Y, Krupenko SA. Chem Biol Interact 191 129-136 (2011)
  7. Mechanistic implications of the cysteine-nicotinamide adduct in aldehyde dehydrogenase based on quantum mechanical/molecular mechanical simulations. Wymore T, Deerfield DW, Hempel J. Biochemistry 46 9495-9506 (2007)
  8. Vascular bioactivation of nitroglycerin by aldehyde dehydrogenase-2: reaction intermediates revealed by crystallography and mass spectrometry. Lang BS, Gorren AC, Oberdorfer G, Wenzl MV, Furdui CM, Poole LB, Mayer B, Gruber K. J Biol Chem 287 38124-38134 (2012)
  9. The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+/enzyme interactions. Langendorf CG, Key TL, Fenalti G, Kan WT, Buckle AM, Caradoc-Davies T, Tuck KL, Law RH, Whisstock JC. PLoS One 5 e9280 (2010)
  10. Crystallographic evidence for active-site dynamics in the hydrolytic aldehyde dehydrogenases. Implications for the deacylation step of the catalyzed reaction. Muñoz-Clares RA, González-Segura L, Díaz-Sánchez AG. Chem Biol Interact 191 137-146 (2011)
  11. Acyl carrier protein-specific 4'-phosphopantetheinyl transferase activates 10-formyltetrahydrofolate dehydrogenase. Strickland KC, Hoeferlin LA, Oleinik NV, Krupenko NI, Krupenko SA. J Biol Chem 285 1627-1633 (2010)
  12. Evaluation of the energetics of the concerted acid-base mechanism in enzymatic catalysis: the case of ketosteroid isomerase. Fried SD, Boxer SG. J Phys Chem B 116 690-697 (2012)
  13. Novel NADPH-cysteine covalent adduct found in the active site of an aldehyde dehydrogenase. Díaz-Sánchez AG, González-Segura L, Rudiño-Piñera E, Lira-Rocha A, Torres-Larios A, Muñoz-Clares RA. Biochem J 439 443-452 (2011)
  14. Phylogeny and evolution of aldehyde dehydrogenase-homologous folate enzymes. Strickland KC, Holmes RS, Oleinik NV, Krupenko NI, Krupenko SA. Chem Biol Interact 191 122-128 (2011)
  15. Structural basis for a cofactor-dependent oxidation protection and catalysis of cyanobacterial succinic semialdehyde dehydrogenase. Park J, Rhee S. J Biol Chem 288 15760-15770 (2013)
  16. The quaternary structure of Thermus thermophilus aldehyde dehydrogenase is stabilized by an evolutionary distinct C-terminal arm extension. Hayes K, Noor M, Djeghader A, Armshaw P, Pembroke T, Tofail S, Soulimane T. Sci Rep 8 13327 (2018)
  17. Amino acid residues that affect the basicity of the catalytic glutamate of the hydrolytic aldehyde dehydrogenases. Muñoz-Clares RA, González-Segura L, Riveros-Rosas H, Julián-Sánchez A. Chem Biol Interact 234 45-58 (2015)
  18. Structure and biochemistry of phenylacetaldehyde dehydrogenase from the Pseudomonas putida S12 styrene catabolic pathway. Crabo AG, Singh B, Nguyen T, Emami S, Gassner GT, Sazinsky MH. Arch Biochem Biophys 616 47-58 (2017)
  19. Aldehyde dehydrogenase homologous folate enzymes: Evolutionary switch between cytoplasmic and mitochondrial localization. Krupenko NI, Holmes RS, Tsybovsky Y, Krupenko SA. Chem Biol Interact 234 12-17 (2015)
  20. Mechanisms of protection against irreversible oxidation of the catalytic cysteine of ALDH enzymes: Possible role of vicinal cysteines. Muñoz-Clares RA, González-Segura L, Murillo-Melo DS, Riveros-Rosas H. Chem Biol Interact 276 52-64 (2017)
  21. The mechanism of discrimination between oxidized and reduced coenzyme in the aldehyde dehydrogenase domain of Aldh1l1. Tsybovsky Y, Malakhau Y, Strickland KC, Krupenko SA. Chem Biol Interact 202 62-69 (2013)
  22. A variety of electrostatic interactions and adducts can activate NAD(P) cofactors for hydride transfer. Meijers R, Cedergren-Zeppezauer E. Chem Biol Interact 178 24-28 (2009)
  23. Catalytic properties of a bacterial acylating acetaldehyde dehydrogenase: evidence for several active oligomeric states and coenzyme A activation upon binding. Fischer B, Boutserin S, Mazon H, Collin S, Branlant G, Gruez A, Talfournier F. Chem Biol Interact 202 70-77 (2013)
  24. Inhibition of homoserine dehydrogenase by formation of a cysteine-NAD covalent complex. Ogata K, Yajima Y, Nakamura S, Kaneko R, Goto M, Ohshima T, Yoshimune K. Sci Rep 8 5749 (2018)
  25. Structure and mechanism of benzaldehyde dehydrogenase from Pseudomonas putida ATCC 12633, a member of the Class 3 aldehyde dehydrogenase superfamily. Zahniser MPD, Prasad S, Kneen MM, Kreinbring CA, Petsko GA, Ringe D, McLeish MJ. Protein Eng Des Sel 30 271-278 (2017)
  26. Structures of the hydrolase domain of zebrafish 10-formyltetrahydrofolate dehydrogenase and its complexes reveal a complete set of key residues for hydrolysis and product inhibition. Lin CC, Chuankhayan P, Chang WN, Kao TT, Guan HH, Fun HK, Nakagawa A, Fu TF, Chen CJ. Acta Crystallogr D Biol Crystallogr 71 1006-1021 (2015)
  27. Kinetic and structural insights into enzymatic mechanism of succinic semialdehyde dehydrogenase from Cyanothece sp. ATCC51142. Xie C, Li ZM, Bai F, Hu Z, Zhang W, Li Z. PLoS One 15 e0239372 (2020)
  28. Reaction of the catalytic cysteine of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa with arsenite-BAL and phenylarsine oxide. González-Segura L, Mújica-Jiménez C, Muñoz-Clares RA. Chem Biol Interact 178 64-69 (2009)
  29. Catalytic contribution of threonine 244 in human ALDH2. González-Segura L, Ho KK, Perez-Miller S, Weiner H, Hurley TD. Chem Biol Interact 202 32-40 (2013)
  30. Cloning and molecular characterization of the betaine aldehyde dehydrogenase involved in the biosynthesis of glycine betaine in white shrimp (Litopenaeus vannamei). Delgado-Gaytán MF, Rosas-Rodríguez JA, Yepiz-Plascencia G, Figueroa-Soto CG, Valenzuela-Soto EM. Chem Biol Interact 276 65-74 (2017)
  31. Gamma glutamyl semialdehyde dehydrogenase: simulations on native and mutant forms support the importance of outer shell lysines. Hempel J, Kraut A, Wymore T. Chem Biol Interact 178 75-78 (2009)
  32. Abnormal downregulation of 10-formyltetrahydrofolate dehydrogenase promotes the progression of oral squamous cell carcinoma by activating PI3K/Akt/Rb pathway. Qu Y, He Y, Ruan H, Qin L, Han Z. Cancer Med 12 5781-5797 (2023)
  33. Crystal structure of yeast xylose reductase in complex with a novel NADP-DTT adduct provides insights into substrate recognition and catalysis. Paidimuddala B, Mohapatra SB, Gummadi SN, Manoj N. FEBS J 285 4445-4464 (2018)
  34. Contribution of conserved Glu255 and Cys289 residues to catalytic activity of recombinant aldehyde dehydrogenase from Bacillus licheniformis. Lee YC, Lin DT, Ong PL, Chen HL, Lo HF, Lin LL. Biochemistry (Mosc) 76 1233-1241 (2011)
  35. Crystal structure of the γ-hydroxymuconic semialdehyde dehydrogenase from Pseudomonas sp. strainWBC-3, a key enzyme involved in para-Nitrophenol degradation. Su J, Zhang C, Zhang JJ, Wei T, Zhu D, Zhou NY, Gu Lc. BMC Struct Biol 13 30 (2013)
  36. Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex. Zheng D, Nakabayashi M, Asano Y. J Biol Chem 298 101650 (2022)
  37. Structure of putative tumor suppressor ALDH1L1. Tsybovsky Y, Sereda V, Golczak M, Krupenko NI, Krupenko SA. Commun Biol 5 3 (2022)
  38. The Active Site of the Enzyme 10-Formyl-THFDH in the Honey Bee Apis mellifera-A Key Player in Formic Acid Detoxification. Mating M, Zou Y, Sharbati S, Einspanier R. Int J Mol Sci 24 354 (2022)


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