Amino acid residues that affect the basicity of the catalytic glutamate of the hydrolytic aldehyde dehydrogenases

Chemico-Biological Interactions

Volumn 234, Issue , 2015, Pages 45-58

  Muñoz Clares, Rosario A ^a   González Segura, Lilian ^a   Riveros Rosas, Héctor ^b   Julián Sánchez, Adriana ^b  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^b UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDE DEHYDROGENASE; AMINO ACID; GLUTAMIC ACID;

BINDING SITE; CATALYSIS; CHEMICAL STRUCTURE; ENZYME ACTIVE SITE; HUMAN; HYDROGEN BOND; HYDROLYSIS; KINETICS; METABOLISM; PROTEIN CONFORMATION;

ALDEHYDE DEHYDROGENASE; AMINO ACIDS; BINDING SITES; CATALYSIS; CATALYTIC DOMAIN; GLUTAMIC ACID; HUMANS; HYDROGEN BONDING; HYDROLYSIS; KINETICS; MODELS, MOLECULAR; PROTEIN CONFORMATION;

EID: 84933525893     PISSN: 00092797     EISSN: 18727786     Source Type: Journal    
DOI: 10.1016/j.cbi.2015.01.019     Document Type: Article

References (57)

1. S. Michels, S. Scagliarini, F. Della Seta, C. Carles, M. Riva, P. Trost, and G. Branlant Arguments against a close relationship between non-phosphorylating and phosphorylating glyceraldehyde-3-phosphate dehydrogenases FEBS Lett. 339 1994 97 100
2. R.A. Muñoz-Clares, A.G. Díaz-Sánchez, L. González-Segura, and C. Montiel Kinetic and structural features of betaine aldehyde dehydrogenases: mechanistic and regulatory implications Arch. Biochem. Biophys. 493 2010 71 81
3. S. Marchal, and G. Branlant Evidence for the chemical activation of essential Cys-302 upon cofactor binding to nonphosphorylating glyceraldehyde 3-posphate dehydrogenase from Streptococcus mutans Biochemistry 38 1999 12950 12958
4. S. Marchal, S. Rahuel-Clermont, and G. Branlant Role of glutamate-268 in the catalytic mechanism of nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans Biochemistry 39 2000 3327 3335
5. K. D'Ambrosio, A. Pailot, F. Talfournier, C. Didierjean, E. Benedetti, A. Aubry, G. Branlant, and C. Corbier The first crystal structure of a thioacylenzyme intermediate in the ALDH family: new coenzyme conformation and relevance to catalysis Biochemistry 45 2006 2978 2986
6. + and a novel cation binding site J. Mol. Biol. 385 2009 542 557
7. R.A. Muñoz-Clares, L. González-Segura, and A.G. Díaz-Sánchez Crystallographic evidence for active-site dynamics in the hydrolytic aldehyde dehydrogenases. Implications for the deacylation step of the catalyzed reaction Chem. Biol. Interact. 191 2011 137 146
8. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta 658 Crystallogr. D 60 2004 2126 2132
9. E. Chovancova, A. Pavelka, P. Benes, O. Strnad, J. Brezovsky, B. Kozlikova, A. Gora, V. Sustr, M. Klvana, and P. Medek CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures PLoS Comput. Biol. 8 2012 e1002708
10. a predictions J. Chem. Theory Comput. 7 2011 525 537
11. a values J. Chem. Theory Comput. 7 2011 2284 2295
12. E. Jain, A. Bairoch, S. Duvaud, I. Phan, N. Redaschi, B.E. Suzek, M.J. Martin, P. McGarv, and E. Gasteiger Infrastructure for the life sciences: design and implementation of the UniProt website BMC Bioinformatics 10 2009 136
13. K. Tamura, G. Stecher, D. Peterson, A. Filipski, and S. Kumar MEGA6: molecular evolutionary genetics analysis version 6.0 Mol. Biol. Evol. 30 2013 2725 2729
14. M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson, and D.G. Higgins Clustal W and clustal X version 2.0 Bioinformatics 23 2007 2947 2948
15. A.I. Roca, A.C. Abajian, and D.J. Vigerust ProfileGrids solve the large alignment visualization problem: influenza hemeagglutinin example F1000 Res. 2 2013 2
16. V. Vasiliou, A. Bairoch, K.F. Tipton, and D.W. Nebert Eukaryotic aldehyde dehydrogenase (ALDH) genes: human polymorphisms, and recommended nomenclature based on divergent evolution and chromosomal mapping Pharmacogenet. Genom. 9 1999 421 434
17. W. Black, and V. Vasiliou The aldehyde dehydrogenase gene superfamily resource center Hum. Genomics. 4 2009 136 142
18. X. Peng, K. Shindo, K. Kanoh, Y. Inomata, S.-K. Choi, and N. Misawa Characterization of Sphingomonas aldehyde dehydrogenase catalyzing the conversion of various aromatic aldehydes to their carboxylic acids Appl. Microbiol. Biotechnol. 69 2005 141 150
19. H. Riveros-Rosas, L. González-Segura, A. Julián-Sánchez, A.G. Díaz-Sánchez, and R.A. Muñoz-Clares Structural determinants of substrate specificity in aldehyde dehydrogenases Chem. Biol. Interact. 202 2013 51 61
20. J. Boch, G. Nau-Wagner, S. Kneip, and E. Bremer Glycine betaine aldehyde dehydrogenase from Bacillus subtilis: characterization of an enzyme required for the synthesis of the osmoprotectant glycine betaine Arch. Microbiol. 168 1997 282 289
21. R. Rosenstein, D. Futter-Bryniok, and F. Gotz The choline-converting pathway in Staphylococcus xylosus C2A: genetic and physiological characterization J. Bacteriol. 181 1999 2273 2278
22. N.N. Samsonova, S.V. Smirnov, A.E. Novikova, and L.R. Ptitsyn Identification of Escherichia coli K12 YdcW protein as a gamma-aminobutyraldehyde dehydrogenase FEBS Lett. 579 2005 4107 4112
23. A. Gruez, V. Roig-Zamboni, S. Grisel, A. Salomoni, C. Valencia, V. Campanacci, M. Tegoni, and C. Cambillau Crystal structure and kinetics identify Escherichia coli ydcW gene product as a medium-chain aldehyde dehydrogenase J. Mol. Biol. 343 2004 29 41
24. A. Jann, H. Matsumoto, and D. Haas The fourth arginine catabolic pathway of Pseudomonas aeruginosa J. Gen. Microbiol. 134 1988 1043 1053
25. Z. Yang, and C.D. Lu Functional genomics enables identification of genes of the arginine transaminase pathway in Pseudomonas aeruginosa J. Bacteriol. 189 2007 3945 3953
26. S. Kurihara, S. Oda, K. Kato, H.G. Kim, T. Koyanagi, H. Kumagai, and H. Suzuki A novel putrescine utilization pathway involves gamma-glutamylated intermediates of Escherichia coli K-12 J. Biol. Chem. 280 2005 4602 4608
27. G.E. Crooks, G. Hon, J.M. Chandonia, and S.E. Brenner WebLogo: a sequence logo generator Genome Res. 14 2004 1188 1190
28. 1-pyrroline-5-carboxylate dehydrogenase J. Mol. Biol. 362 2006 490 501
29. A.G. Díaz-Sánchez, L. González-Segura, C. Mújica-Jiménez, E. Rudiño-Piñera, C. Montiel, L.P. Martínez-Castilla, and R.A. Muñoz-Clares Amino acid residues critical for the specificity for betaine aldehyde of the plant ALDH10 isoenzyme involved in the synthesis of glycine betaine Plant Physiol. 158 2012 1570 1582
30. C. Chen, J.C. Joo, G. Brown, E. Stolnikova, A.S. Halavaty, A. Savchenko, W.F. Anderson, and A.F. Yakunin Substrate inhibition of the betaine aldehyde dehydrogenase BetB from Staphylococcus aureus: structure-based mutational studies Appl. Environ. Microbiol. 80 2014 3992 4002
31. Y.G. Kim, S. Lee, O.S. Kwon, S.Y. Park, S.J. Lee, B.J. Park, and K.J. Kim Redox-switch modulation of human SSADH by dynamic catalytic loop EMBO J. 28 2009 959 968
32. Z. Yuan, B. Yin, D. Wei, and Y.R. Yuan Structural basis for cofactor and substrate selection by cyanobacterium succinic semialdehyde dehydrogenase J. Struct. Biol. 182 2013 125 135
33. Y. Saito, Y. Ishii, H. Hayashi, Y. Imao, T. Akashi, K. Yoshikawa, Y. Noguchi, S. Soeda, M. Yoshida, M. Niwa, J. Hosoda, and K. Shimomura Cloning of genes coding for L-sorbose and L-sorbosone dehydrogenases from Gluconobacter oxydans and microbial production of 2-keto-L-gulonate, a precursor of L-ascorbic acid, in a recombinant G. oxydans strain Appl. Environ. Microbiol. 63 1997 454 460
34. + oxidoreductase Appl. Biochem. Biotechnol. 98-100 2002 415 428
35. S. Kühner, L. Wöhlbrand, I. Fritz, W. Wruck, C. Hultschig, P. Hufnagel, M. Kube, R. Reinhardt, and R. Rabus Substrate-dependent regulation of anaerobic degradation pathways for toluene and ethylbenzene in a denitrifying bacterium, strain EbN1 J. Bacteriol. 187 2005 1493 1503
36. S. Marchal, and G. Branlant Characterization of the amino acids involved in substrate specificity of nonphosphorylating glyceraldehydes-3-phosphate dehydrogenase from Streptococcus mutans J. Biol. Chem. 42 2002 39235 39242
37. R.I. Feldman, and H. Weiner Horse liver aldehyde dehydrogenase. II. Kinetics and mechanistic implications of the dehydrogenase and esterase activity J. Biol. Chem. 247 1972 267 272
38. R.C. Vallari, and R. Pietruszko Kinetic mechanism of the human cytoplasmic aldehyde dehydrogenase E1 Arch. Biochem. Biophys. 212 1981 9 19
39. A.J. Rivett, and K.F. Tipton Kinetic studies with rat-brain succinic-semialdehyde dehydrogenase Eur. J. Biochem. 117 1981 187 193
40. E.M. Valenzuela-Soto, and R.A. Muñoz-Clares Betaine-aldehyde dehydrogenase from leaves of Amaranthus hypochondriacus L. exhibits an iso ordered Bi Bi steady state mechanism J. Biol. Chem. 268 1993 23818 23823 (Erratum: J. Biol. Chem. 269 (1994) 4692)
41. +-dependent reactions catalysed by betaine aldehyde dehydrogenase from Pseudomonas aeruginosa Biochem. J. 352 2000 675 683
42. C.G. Steinmetz, P. Xie, H. Weiner, and T.D. Hurley Structure of mitochondrial aldehyde dehydrogenase: the genetic component of ethanol aversion Structure 5 1997 701 711
43. S.J. Perez-Miller, and T.D. Hurley Coenzyme isomerization is integral to catalysis in aldehyde dehydrogenase Biochemistry 42 2003 7100 7109
44. Y. Tsybovsky, H. Donato, N.I. Krupenko, C. Davies, and S.A. Krupenko Crystal structures of the carboxyl terminal domain of rat 10-formyltetrahydrofolate dehydrogenase: implications for the catalytic mechanism of aldehyde dehydrogenases Biochemistry 46 2007 2917 2929
45. D. Cobessi, F. Tête-Favier, S. Marchal, G. Branlant, and A. Aubry Structural and biochemical investigations of the catalytic mechanism of an NADP-dependent aldehyde dehydrogenase from Streptococcus mutans J. Mol. Biol. 300 2000 141 152
46. X. Wang, and H. Weiner Involvement of glutamate 268 in the active site of human liver mitochondrial (class 2) aldehyde dehydrogenase as probed by site-directed mutagenesis Biochemistry 34 1995 237 243
47. M. Vedadi, and E. Meighen Critical glutamic residues affecting the mechanism and nucleotide specificity of Vibrio harveyi aldehyde dehydrogenase Eur. J. Biochem. 246 1997 698 704
48. C.J. Mann, and H. Weiner Differences in the roles of conserved glutamic acid residues in the active site of human class 3 and class 2 aldehyde dehydrogenases Protein Sci. 8 1999 1922 1929
49. B. Wei, D.C. Mays, J.J. Lipsky, and H. Weiner Chemical modifications to study mutations that affect the ability of the general base (E268) to function in human liver mitochondrial aldehyde dehydrogenase Chem. Biol. Interact. 143-144 2003 85 91
50. K. Takahashi, and H. Weiner Nicotinamide adenine dinucleotide activation of the esterase reaction of horse liver aldehyde dehydrogenase Biochemistry 20 1981 2720 2726
51. K. Johansson, M. El-Ahmad, S. Ramaswamy, L. Hjelmqvist, H. Jörnvall, and H. Eklund Structure of betaine aldehyde dehydrogenase at 2.1 Å resolution Protein Sci. 87 1998 2106 2117
52. T. Wymore, J. Hempel, S.S. Cho, A.D. MacKerell, H.B. Nicholas Jr, and D.W. Deerfield Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation Proteins 57 2004 758 771
53. E. Lorentzen, R. Hensel, T. Knura, H. Ahmed, and E. Pohl Structural basis of allosteric regulation and substrate specificity of the non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase from Thermoproteus tenax J. Mol. Biol. 341 2004 815 828
54. Y.V.G. Schlippe, and L. Hedstrom A twisted base? The role of arginine in enzyme-catalyzed proton abstractions Arch. Biochem. Biophys. 433 2005 266 278
55. K. Takahashi, H. Weiner, and D.L. Filmer Effects of pH on horse liver aldehyde dehydrogenase: alterations in metal ion activation, number of functioning active sites, and hydrolysis of the acyl intermediate Biochemistry 20 1981 6225 6230
56. F.M. Dickinson Studies on the mechanism of sheep liver cytosolic aldehyde dehydrogenase. The effect of pH on the aldehyde binding reactions and a re-examination of the problem of the site of proton release in the mechanism Biochem. J. 238 1986 75 82
57. C.E. Graham, K. Brocklehurst, R.W. Pickersgill, and M.J. Warren Characterization of retinaldehyde dehydrogenase 3 Biochem. J. 394 2006 67 75