Redesign of coenzyme B 12 dependent diol dehydratase to be resistant to the mechanism-based inactivation by glycerol and act on longer chain 1,2-diols

FEBS Journal

Volumn 279, Issue 5, 2012, Pages 793-804

  Yamanishi, Mamoru ^a   Kinoshita, Koichiro ^a   Fukuoka, Masaki ^a   Saito, Takuya ^a   Tanokuchi, Aya ^a   Ikeda, Yuuki ^a   Obayashi, Hirokazu ^a   Mori, Koichi ^a   Shibata, Naoki ^b,c   Tobimatsu, Takamasa ^a   Toraya, Tetsuo ^a  

^a OKAYAMA UNIVERSITY   (Japan)

^b UNIVERSITY OF HYOGO   (Japan)

^c RIKEN HARIMA INSTITUTE   (Japan)

Author keywords

adenosylcobalamin; coenzyme B 12; diol dehydratase; mechanism based inactivation; redesign of enzyme; X ray structure

Indexed keywords

COBAMAMIDE; DIOL DEHYDRATASE; GLYCEROL; HYDROLYASE; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME CONFORMATION; ENZYME INACTIVATION; ENZYME MECHANISM; ENZYME MODIFICATION; ENZYME SUBSTRATE; PRIORITY JOURNAL; STEREOSPECIFICITY; STRUCTURE ANALYSIS; WILD TYPE;

CATALYSIS; CATALYTIC DOMAIN; COBAMIDES; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DRUG RESISTANCE; GLYCEROL; KINETICS; KLEBSIELLA OXYTOCA; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROPANEDIOL DEHYDRATASE; PROPYLENE GLYCOL; PROTEIN CONFORMATION; STEREOISOMERISM; VITAMIN B 12;

EID: 84857655713     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2012.08470.x     Document Type: Article

References (46)

1. Lee HA Jr, &, Abeles RH, (1963) Purification and properties of dioldehydrase, an enzyme requiring a cobamide coenzyme. J Biol Chem 238, 2367-2373.
2. 12-dependent diol dehydrase: glycerol as both a good substrate and a potent inactivator. Biochem Biophys Res Commun 69, 475-480.
3. 12-dependent isomerization (eliminating) reactions. Chem Rev 103, 2095-2127.
4. 12-dependent diol dehydratase: regulation of apoenzyme synthesis in Klebsiella pneumoniae (Aerobacter aerogenes) ATCC 8724. J Bacteriol 135, 726-729. (Pubitemid 9000296)
5. 12-dependent diol dehydratase and glycerol dehydratase in selected genera of Enterobacteriaceae and Propionibacteriaceae. J Bacteriol 141, 1439-1442. (Pubitemid 10074779)
6. Forage RG, &, Foster MA, (1979) Resolution of the coenzyme B-12-dependent dehydratases of Klebsiella sp. and Citrobacter freundii. Biochim Biophys Acta 569, 249-258. (Pubitemid 9237882)
7. Bachovchin WW, Eagar RG Jr, Moore KW, &, Richards JH, (1977) Mechanism of action of adenosylcobalamin: glycerol and other substrate analogues as substrates and inactivators for propanediol dehydratase-kinetics, stereospecificity, and mechanism. Biochemistry 16, 1082-1092. (Pubitemid 8062242)
8. Schneider Z, &, Pawelkiewicz J, (1966) The properties of glycerol dehydratase isolated from Aerobacter aerogenes, and the properties of the apoenzyme subunits. Acta Biochim Pol 13, 311-328.
9. Poznanskaya AA, Yakusheva MI, &, Yakovlev VA, (1977) Study of the mechanism of action of adenosylcobalamin-dependent glycerol dehydratase from Aerobacter aerogenes. II. The inactivation kinetics of glycerol dehydratase complexes with adenosylcobalamin and its analogs. Biochim Biophys Acta 484, 236-243. (Pubitemid 8169853)
10. 12-dependent enzymes, glycerol dehydratase and diol dehydratase. J Bacteriol 143, 1458-1465. (Pubitemid 11254947)
11. 12-dependent enzymes, glycerol dehydratase and diol dehydratase. J Nutr Sci Vitaminol 28, 225-236. (Pubitemid 12033790)
12. Mori K, Tobimatsu T, Hara T, &, Toraya T, (1997) Characterization, sequencing, and expression of the genes encoding a reactivating factor for glycerol-inactivated adenosylcobalamin-dependent diol dehydratase. J Biol Chem 272, 32034-32041. (Pubitemid 28011871)
13. 12-dependent diol dehydratase. J Biol Chem 274, 3372-3377. (Pubitemid 29077174)
14. 12-dependent diol dehydratase by a molecular chaperone-like reactivating factor. Biochemistry 38, 13170-13178.
15. Tobimatsu T, Kajiura H, Yunoki M, Azuma M, &, Toraya T, (1999) Identification and expression of the genes encoding a reactivating factor for adenosylcobalamin-dependent glycerol dehydratase. J Bacteriol 181, 4110-4113. (Pubitemid 29295933)
16. Kajiura H, Mori K, Tobimatsu T, &, Toraya T, (2001) Characterization and mechanism of action of a reactivating factor for adenosylcobalamin-dependent glycerol dehydratase. J Biol Chem 276, 36514-36519.
17. 12-dependent glycerol dehydratase of Citrobacter freundii. Eur J Biochem 268, 2369-2378. (Pubitemid 32417766)
18. Kajiura H, Mori K, Shibata N, &, Toraya T, (2007) Molecular basis for specificities of reactivating factors for adenosylcobalamin-dependent diol and glycerol dehydratases. FEBS J 274, 5556-5566. (Pubitemid 47622067)
19. Mori K, Hosokawa Y, Yoshinaga T, &, Toraya T, (2010) Diol dehydratase-reactivating factor is a reactivase: evidence for multiple turnovers and subunit swapping with diol dehydratase. FEBS J 277, 4931-4943.
20. 12: X-ray structure of a diol-dehydratase-adeninylpentylcobalamin complex. Structure 8, 775-788. (Pubitemid 30469995)
21. 12-dependent diol dehydratase. J Biol Chem 278, 22717-22725. (Pubitemid 36830331)
22. 12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase. Structure 7, 997-1008. (Pubitemid 29372521)
23. 12- dependent diol dehydratase is a potassium ion-requiring calcium metalloenzyme: evidence that the substrate-coordinated metal ion is calcium. Biochemistry 49, 7210-7217.
24. 12-dependent glycerol dehydratase in complex with cobalamin and propane-1,2-diol. Eur J Biochem 269, 4484-4494.
25. 12-dependent diol dehydratase. J Biol Chem 281, 18327-18334. (Pubitemid 44035489)
26. Zagalak B, Frey PA, Karabatsos GL, &, Abeles RH, (1966) The stereochemistry of the conversion of D and L 1,2-propanediols to propionaldehyde. J Biol Chem 241, 3028-3035.
27. Rétey J, Umani-Ronchi A, Seibl J, &, Arigoni D, (1966) On the mechanism of the propanediol dehydrase reaction. Experientia 22, 502-503.
28. Yamane T, Kato T, Shimizu S, &, Fukui S, (1966) Comparison of reactivity between D-propanediol and L-propanediol in intramolecular oxidation-reduction catalyzed by dioldehydrase requiring cobamide coenzyme. Arch Biochem Biophys 113, 362-366.
29. Jensen FR, &, Neese RA, (1975) Relative enantiomer binding and reaction rates with propanediol dehydrase. Biochem Biophys Res Commun 62, 816-821.
30. Tobimatsu T, Hara T, Sakaguchi M, Kishimoto Y, Wada Y, Isoda M, Sakai T, &, Toraya T, (1995) Molecular cloning, sequencing, and expression of the genes encoding adenosylcobalamin-dependent diol dehydrase of Klebsiella oxytoca. J Biol Chem 270, 7142-7148.
31. Tobimatsu T, Sakai T, Hashida Y, Mizoguchi N, Miyoshi S, &, Toraya T, (1997) Heterologous expression, purification, and properties of diol dehydratase, an adenosylcobalamin-dependent enzyme of Klebsiella oxytoca. Arch Biochem Biophys 347, 132-140. (Pubitemid 27484030)
32. Otwinowski Z, &, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276, 307-326. (Pubitemid 27085611)
33. French S, &, Wilson K, (1978) On the treatment of negative intensity observations. Acta Crystallogr A 34, 517-525.
34. Collaborative Computational Project Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50, 760-763.
35. Brunger AT, (2007) Version 1.2 of the crystallography and NMR system. Nat Protoc 2, 2728-2733.
36. Emsley P, &, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132. (Pubitemid 41742764)
37. Chen VB, Arendall WB III, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, &, Richardson DC, (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66, 12-21.
38. Tobimatsu T, Kawata M, &, Toraya T, (2005) The N-terminal regions of β and Î subunits lower the solubility of adenosylcobalamin-dependent diol dehydratase. Biosci Biotechnol Biochem 69, 455-462. (Pubitemid 40589102)
39. Toraya T, Ushio K, Fukui S, &, Hogenkamp HPC, (1977) Studies on the mechanism of the adenosylcobalamin-dependent diol dehydrase reaction by the use of analogs of the coenzyme. J Biol Chem 252, 963-970. (Pubitemid 8041890)
40. 12 coenzymes in the reaction catalyzed by dioldehydrase. Biochemistry 18, 417-426.
41. + oxidoreductase. J Bacteriol 169, 2050-2054. (Pubitemid 17081766)
42. Gill SC, &, von Hippel PH, (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem 182, 319-326. (Pubitemid 19277112)
43. Davis BJ, (1964) Disc electrophoresis. II. Method and application to human serum proteins. Ann NY Acad Sci 121, 404-427.
44. Laemmli UK, (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 227, 680-685.
45. Kraulis J, (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24, 946-950.
46. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, &, Ferrin TE, (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25, 1605-1612.