Discovery of a cytokinin deaminase

ACS Chemical Biology

Volumn 6, Issue 10, 2011, Pages 1036-1040

  Goble, Alissa M ^a   Fan, Hao ^b   Sali, Andrej ^b   Raushel, Frank M ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE DERIVATIVE; ADENOSINE; CYTOKININ; CYTOKININ DEAMINASE; DEAMINASE; GENOMIC DNA; GUANINE DERIVATIVE; METHYLAMINE; PHYTOHORMONE; PURINE DERIVATIVE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; DEAMINATION; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME STRUCTURE; ENZYME SUBSTRATE; HYDROLYSIS; MOLECULAR CLONING; MOLECULAR DOCKING; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PSEUDOALTEROMONAS;

ADENINE; AMINOHYDROLASES; CYTOKININS; DEAMINATION; MODELS, MOLECULAR; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA; SUBSTRATE SPECIFICITY;

PSEUDOALTEROMONAS ATLANTICA;

EID: 80055002526     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb200198c     Document Type: Article

References (32)

1. Seibert, C. M. and Raushel, F. M. (2005) Structural and catalytic diversity within the amidohydrolase superfamily Biochemistry 44, 6383-6391 (Pubitemid 40593789)
2. Ho, M. C., Cassera, M. B., Madrid, D. C., Ting, L. M., Tyler, P. C., Kim, K., Almo, S. C., and Schramm, V. L. (2009) Structural and metabolic specificity of methylthiocoformycin for malarial adenosine deaminases Biochemistry 48, 9618-9626
3. Kamat, S. S., Fan, H., Sauder, J. M., Burley, S. K., Shoichet, B. K., Sali, A., and Raushel, F. M. (2011) Enzymatic deamination of the epigenetic base N-6-methyladenine J. Am. Chem. Soc. 133, 2080-2083
4. Hall, R. S., Agarwal, R., Hitchcock, D., Sauder, J. M., Burley, S. K., Swaminathan, S., and Raushel, F. M. (2010) Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase Biochemistry 49, 4374-4382
5. Atkinson, H. J., Morris, J. H., Ferrin, T. E., and Babbitt, P. C. (2009) Using sequence similarity networks for visualization of relationships across diverse protein superfamilies PLoS One 4, e4345
6. Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 13, 2498-2504 (Pubitemid 37428274)
7. Goble, A. M., Zhang, Z., Sauder, J. M., Burley, S. K., Swaminathan, S., and Raushel, F. M. (2011) Pa0148 from Pseudomonas aeruginosa catalyzes the deamination of adenine Biochemistry 50, 6589-6597
8. Yaphe, W. (1957) The use of agarase from Pseudomonas atlantica in the identification of agar in marine algae (Rhodophyceae) Can. J. Microbiol. 3, 987-993
9. Bergmeyer, H. U., Ed. (1974) Methods of Enzymatic Analysis, Academic Press, New York, NY.
10. Sali, A. and Blundell, T. L. (1993) Comparative protein modeling by satisfaction of spatial restraints J. Mol. Biol. 234, 779-815 (Pubitemid 24007801)
11. Tubbs, J. L., Latypov, V., Kanugula, S., Butt, A., Melikishvili, M., Kraehenbuehl, R., Fleck, O., Marriott, A., Watson, A. J., Verbeek, B., McGown, G., Thorncroft, M., Santibanez-Koref, M. F., Millington, C., Arvai, A. S., Kroeger, M. D., Peterson, L. A., Williams, D. M., Fried, M. G., Margison, G. P., Pegg, A. E., and Tainer, J. A. (2009) Flipping of alkylated DNA damage bridges base and nucleotide excision repair Nature 459, 808-813
12. Hermann, J. C., Ghanem, E., Li, Y. C., Raushel, F. M., Irwin, J. J., and Shoichet, B. K. (2006) Predicting substrates by docking high-energy intermediates to enzyme structures J. Am. Chem. Soc. 128, 15882-15891 (Pubitemid 44894131)
13. Hermann, J. C., Marti-Arbona, R., Fedorov, A. A., Fedorov, E., Almo, S. C., Shoichet, B. K., and Raushel, F. M. (2007) Structure-based activity prediction for an enzyme of unknown function Nature 448, 775-U772
14. Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Res. 28, 27-30 (Pubitemid 30047706)
15. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K. F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M. (2006) From genomics to chemical genomics: new developments in KEGG Nucleic Acids Res. 34, D354-D357
16. Lorber, D. M. and Shoichet, B. K. (2005) Hierarchical docking of databases of multiple ligand conformations Curr. Top. Med. Chem. 5, 739-749 (Pubitemid 41179714)
17. Meng, E. C., Shoichet, B. K., and Kuntz, I. D. (1992) Automated docking with grid-based energy evaluation J. Comput. Chem. 13, 505-524
18. Mohamedali, K. A., Kurz, L. C., and Rudolph, F. B. (1996) Site-directed mutagenesis of active site glutamate-217 in mouse adenosine deaminase Biochemistry 35, 1672-1680 (Pubitemid 26055302)
19. Skoog, F., Hamzi, H. Q., Szweykow, Am, Leonard, N. J., Carraway, K. L., Fujii, T., Helgeson, J. P., and Loeppky, R. N. (1967) Cytokinins-Structure/ Activity Relationships Phytochemistry 6, 1169
20. Yokoya, N. S., Stirk, W. A., van Staden, J., Novak, O., Tureckova, V., Pencik, A., and Strnad, M. (2010) Endogenous cytokinins, auxins, and abscisic acid in red algae from Brazil J. Phycol. 46, 1198-1205
21. Kakimoto, T. (2003) Biosynthesis of cytokinins J. Plant Re.s 116, 233-239 (Pubitemid 36887249)
22. Uziel, M. and Gassen, H. G. (1969) Phenylalanine transfer ribonucleic acid from Escherichia coli B. Isolation and characterization of oligonucleotides from ribonuclease T-1 and ribonuclease A hydrolysates Biochemistry 8, 1643-1655
23. Nishimura, S., Yamada, Y., and Ishikura, H. (1969) The presence of 2-methylthio-N6-(delta-2-isopentenyl) adenosine in serine and phenylalanine transfer RNAs from Escherichia coli Biochim. Biophys. Acta 179, 517-520
24. Chen, C., Smith, O. C., and McChesney, J. (1975) Biosynthesis and cytokinin activity of 8-hydroxy and 2,8-dihydroxy derivatives of zeatin and N-6(increment-2-isopentenyl)adenine Biochemistry 14, 3088-3093
25. Whitty, C. D. and Hall, R. H. (1974) A cytokinin oxidase in Zea mays Can. J. Biochem. 52, 789-799
26. Holmstrom, C. and Kjelleberg, S. (1999) Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents FEMS Microbiol. Ecol. 30, 285-293
27. Morita, R., Nakagawa, N., Kuramitsu, S., and Masui, R. (2008) An O6-methylguanine-DNA methyltransferase-like protein from Thermus thermophilus interacts with a nucleotide excision repair protein J. Biochem. 144, 267-277
28. Schnoes, A. M., Brown, S. D., Dodevski, I., and Babbitt, P. C. (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies PLoS Comput. Biol. 5, e1000605
29. Hall, R. S., Xiang, D. F., Xu, C., and Raushel, F. M. (2007) N-Acetyl- d -glucosamine-6-phosphate deacetylase: substrate activation via a single divalent metal ion Biochemistry 46, 7942-7952 (Pubitemid 47051630)
30. Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32, 1792-1797 (Pubitemid 38832724)
31. Shen, M. Y. and Sali, A. (2006) Statistical potential for assessment and prediction of protein structures Protein Sci. 15, 2507-2524 (Pubitemid 44771688)
32. Sherman, W., Day, T., Jacobson, M. P., Friesner, R. A., and Farid, R. (2006) Novel procedure for modeling ligand/receptor induced fit effects J. Med. Chem. 49, 534-553 (Pubitemid 43157487)