Structure-based redesign of cofactor binding in putrescine oxidase

Biochemistry

Volumn 50, Issue 19, 2011, Pages 4209-4217

  Kopacz, Malgorzata M ^a   Rovida, Stefano ^b   Van Duijn, Esther ^c   Fraaije, Marco W ^a   Mattevi, Andrea ^b  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF PAVIA   (Italy)

^c UTRECHT UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; ALIPHATIC DIAMINES; AMINE OXIDASE; COFACTOR BINDING; COFACTORS; COMPETITIVE BINDING; COVALENT LINKAGE; ENZYME PREPARATION; FLAVOENZYMES; MOLECULAR BASIS; MONOAMINE OXIDASE; MUTANT ENZYMES; PEPTIDE CONFORMATION; PROTEIN MOLECULES; RHODOCOCCUS ERYTHROPOLIS; STRUCTURE-BASED; SUBSTRATE RECOGNITION; SUBSTRATE SPECIFICITY; TERMINAL AMINO GROUPS; WILD TYPES;

BINDING ENERGY; CONFORMATIONS; ENZYMES; FEATURE EXTRACTION; STRUCTURAL ANALYSIS;

SUBSTRATES;

ADENOSINE DIPHOSPHATE; DIAMINE; DINUCLEOTIDE; FLAVINE ADENINE NUCLEOTIDE; MONOMER; OXIDOREDUCTASE; PUTRESCINE OXIDASE; QUERCETIN; TYROSINE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; ELECTROSPRAY MASS SPECTROMETRY; ENZYME ACTIVITY; ENZYME KINETICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; RHODOCOCCUS ERYTHROPOLIS;

ADENOSINE DIPHOSPHATE; BIOCATALYSIS; COENZYMES; CRYSTALLOGRAPHY, X-RAY; FLAVIN-ADENINE DINUCLEOTIDE; HUMANS; MODELS, MOLECULAR; MONOAMINE OXIDASE; MUTAGENESIS, SITE-DIRECTED; OXIDOREDUCTASES ACTING ON CH-NH GROUP DONORS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; RHODOCOCCUS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; STRUCTURE-ACTIVITY RELATIONSHIP;

RHODOCOCCUS ERYTHROPOLIS;

EID: 79955847793     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi200372u     Document Type: Article

References (38)

1. Dym, O. and Eisenberg, D. (2001) Sequence-Structure Analysis of FAD-Containing Proteins Protein Sci. 10, 1712-1728 (Pubitemid 32848768)
2. Heuts, D. P., Scrutton, N. S., McIntire, W. S., and Fraaije, M. W. (2009) Whats in a Covalent Bond? on the Role and Formation of Covalently Bound Flavin Cofactors FEBS J. 276, 3405-3427
3. Mewies, M., McIntire, W. S., and Scrutton, N. S. (1998) Covalent Attachment of Flavin Adenine Dinucleotide (FAD) and Flavin Mononucleotide (FMN) to Enzymes: The Current State of Affairs Protein Sci. 7, 7-20 (Pubitemid 28133742)
4. Kim, J., Fuller, J. H., Kuusk, V., Cunane, L., Chen, Z. W., Mathews, F. S., and McIntire, W. S. (1995) The Cytochrome Subunit is Necessary for Covalent FAD Attachment to the Flavoprotein Subunit of p-Cresol Methylhydroxylase J. Biol. Chem. 270, 31202-31209 (Pubitemid 26018399)
5. Brandsch, R. and Bichler, V. (1991) Autoflavinylation of apo 6-Hydroxy-D-Nicotine Oxidase J. Biol. Chem. 266, 19056-19062
6. Robinson, K. M. and Lemire, B. D. (1996) Covalent Attachment of FAD to the Yeast Succinate Dehydrogenase Flavoprotein Requires Import into Mitochondria, Presequence Removal, and Folding J. Biol. Chem. 271, 4055-4060 (Pubitemid 26070499)
7. Trickey, P., Wagner, M. A., Jorns, M. S., and Mathews, F. S. (1999) Monomeric Sarcosine Oxidase: Structure of a Covalently Flavinylated Amine Oxidizing Enzyme Structure 7, 331-345 (Pubitemid 29159692)
8. van Hellemond, E. W., van Dijk, M., Heuts, D. P., Janssen, D. B., and Fraaije, M. W. (2008) Discovery and Characterization of a Putrescine Oxidase from Rhodococcus erythropolis NCIMB 11540 Appl. Microbiol. Biotechnol. 78, 455-463
9. Edmondson, D. E., Binda, C., Wang, J., Upadhyay, A. K., and Mattevi, A. (2009) Molecular and Mechanistic Properties of the Membrane-Bound Mitochondrial Monoamine Oxidases Biochemistry 48, 4220-4230
10. Atkin, K. E., Reiss, R., Koehler, V., Bailey, K. R., Hart, S., Turkenburg, J. P., Turner, N. J., Brzozowski, A. M., and Grogan, G. (2008) The Structure of Monoamine Oxidase from Aspergillus niger Provides a Molecular Context for Improvements in Activity obtained by Directed Evolution J. Mol. Biol. 384, 1218-1231
11. van Hellemond, E. W., Mazon, H., Heck, A. J., van den Heuvel, R. H., Heuts, D. P., Janssen, D. B., and Fraaije, M. W. (2008) ADP Competes with FAD Binding in Putrescine Oxidase J. Biol. Chem. 283, 28259-28264
12. DeSa, R. J. (1972) Putrescine Oxidase from Micrococcus rubens. Purification and Properties of the Enzyme J. Biol. Chem. 247, 5527-5534
13. Kearney, E. B., Salach, J. I., Walker, W. H., Seng, R. L., Kenney, W., Zeszotek, E., and Singer, T. P. (1971) The Covalently-Bound Flavin of Hepatic Monoamine Oxidase. 1. Isolation and Sequence of a Flavin Peptide and Evidence for Binding at the 8alpha Position Eur. J. Biochem. 24, 321-327
14. Collaborative Computational Project, Number 4. (1994) The CCP4 Suite: Programs for Protein Crystallography. Acta Crystallogr., Sect. D: Biol. Crystallogr. 50, 760-763.
15. Emsley, P., Lohkamp, B., Scott, W. G., and Cowtan, K. (2010) Features and Development of Coot Acta Crystallogr., Sect. D: Biol. Crystallogr. 66, 486-501
16. Potterton, L., McNicholas, S., Krissinel, E., Gruber, J., Cowtan, K., Emsley, P., Murshudov, G. N., Cohen, S., Perrakis, A., and Noble, M. (2004) Developments in the CCP4Molecular-Graphics Project Acta Crystallogr., Sect D: Biol. Crystallogr. 60, 2288-2294
17. Kleywegt, G. J. and Jones, T. A. (1994) Detection, Delineation, Measurement and Display of Cavities in Macromolecular Structures Acta Crystallogr., Sect. D: Biol. Crystallogr. 50, 178-185 (Pubitemid 2054290)
18. Son, S. Y., Ma, J., Kondou, Y., Yoshimura, M., Yamashita, E., and Tsukihara, T. (2008) Structure of Human Monoamine Oxidase A at 2.2-A Resolution: The Control of Opening the Entry for substrates/inhibitors Proc. Natl. Acad. Sci. U.S.A. 105, 5739-5744 (Pubitemid 351758442)
19. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank Nucleic Acids Res. 28, 235-242 (Pubitemid 30047768)
20. Binda, C., Mattevi, A., and Edmondson, D. E. (2002) Structure-Function Relationships in Flavoenzyme-Dependent Amine Oxidations: A Comparison of Polyamine Oxidase and Monoamine Oxidase J. Biol. Chem. 277, 23973-23976 (Pubitemid 34951906)
21. Binda, C., Angelini, R., Federico, R., Ascenzi, P., and Mattevi, A. (2001) Structural Bases for Inhibitor Binding and Catalysis in Polyamine Oxidase Biochemistry 40, 2766-2776 (Pubitemid 32198278)
22. Li, M., Binda, C., Mattevi, A., and Edmondson, D. E. (2006) Functional Role of the "Aromatic Cage" in Human Monoamine Oxidase B: Structures and Catalytic Properties of Tyr435 Mutant Proteins Biochemistry 45, 4775-4784
23. Wierenga, R. K., De Maeyer, M. C. H., and Hol, W. G. J. (1985) Interaction of Pyrophosphate Moieties with.Alpha.-Helixes in Dinucleotide-Binding Proteins Biochemistry 24, 1346-1357
24. Vallon, O. (2000) New Sequence Motifs in Flavoproteins: Evidence for Common Ancestry and Tools to Predict Structure Proteins 38, 95-114 (Pubitemid 30020606)
25. Trickey, P., Basran, J., Lian, L. Y., Chen, Z., Barton, J. D., Sutcliffe, M. J., Scrutton, N. S., and Mathews, F. S. (2000) Structural and Biochemical Characterization of Recombinant Wild Type and a C30A Mutant of Trimethylamine Dehydrogenase from Methylophilus Methylotrophus (Sp. W(3)A(1)) Biochemistry 39, 7678-7688 (Pubitemid 30439596)
26. van den Heuvel, R. H. and Heck, A. J. (2004) Native Protein Mass Spectrometry: From Intact Oligomers to Functional Machineries Curr. Opin. Chem. Biol. 8, 519-526 (Pubitemid 39278349)
27. Miller, J. R. and Edmondson, D. E. (1999) Influence of Flavin Analogue Structure on the Catalytic Activities and Flavinylation Reactions of Recombinant Human Liver Monoamine Oxidases A and B J. Biol. Chem. 274, 23515-23525
28. Zhou, B. P., Lewis, D. A., Kwan, S. W., and Abell, C. W. (1995) Flavinylation of Monoamine Oxidase B J. Biol. Chem. 270, 23653-23660
29. Bruckner, R. C., Zhao, G., Ferreira, P., and Jorns, M. S. (2007) A Mobile Tryptophan is the Intrinsic Charge Transfer Donor in a Flavoenzyme Essential for Nikkomycin Antibiotic Biosynthesis Biochemistry 46, 819-827 (Pubitemid 46133598)
30. Walsh, C. (1980) Flavin Coenzymes: At the Crossroads of Biological Redox Chemistry Acc. Chem. Res. 13, 148-155
31. Efimov, I. and McIntire, W. S. (2004) A Study of the Spectral and Redox Properties and Covalent Flavinylation of the Flavoprotein Component of p-Cresol Methylhydroxylase Reconstituted with FAD Analogues Biochemistry 43, 10532-10546 (Pubitemid 39079324)
32. Koetter, J. W. and Schulz, G. E. (2005) Crystal Structure of 6-Hydroxy-D-Nicotine Oxidase from Arthrobacter nicotinovorans J. Mol. Biol. 352, 418-428 (Pubitemid 41207792)
33. Weyler, W., Hsu, Y. P., and Breakefield, X. O. (1990) Biochemistry and Genetics of Monoamine Oxidase Pharmacol. Ther. 47, 391-417 (Pubitemid 20309559)
34. Hirashiki, I., Ogata, F., and Ito, A. (1995) Rat Monoamine Oxidase B Expressed in Escherichia Coli has a Covalently-Bound FAD Biochem. Mol. Biol. Int. 37, 39-44 (Pubitemid 26177875)
35. Lu, G., Unge, T., Owera-Atepo, J. B., Shih, J. C., Ekblom, J., and Oreland, L. (1996) Characterization and Partial Purification of Human Monoamine Oxidase-B Expressed in Escherichia coli Protein Expression Purif. 7, 315-322 (Pubitemid 26263263)
36. Jin, J., Mazon, H., van den Heuvel, R. H., Heck, A. J., Janssen, D. B., and Fraaije, M. W. (2008) Covalent Flavinylation of Vanillyl-Alcohol Oxidase is an Autocatalytic Process FEBS J. 275, 5191-5200
37. Hassan-Abdallah, A., Bruckner, R. C., Zhao, G., and Jorns, M. S. (2005) Biosynthesis of Covalently Bound Flavin: Isolation and in Vitro Flavinylation of the Monomeric Sarcosine Oxidase Apoprotein Biochemistry 44, 6452-6462 (Pubitemid 40593796)
38. Brizio, C., Brandsch, R., Douka, M., Wait, R., and Barile, M. (2008) The Purified Recombinant Precursor of Rat Mitochondrial Dimethylglycine Dehydrogenase Binds FAD Via an Autocatalytic Reaction Int. J. Biol. Macromol. 42, 455-462