A global characterization and identification of multifunctional enzymes

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Cheng, Xian Ying ^a   Huang, Wei Juan ^a   Hu, Shi Chang ^a   Zhang, Hai Lei ^b   Wang, Hao ^a   Zhang, Jing Xian ^b   Lin, Hong Huang ^b   Chen, Yu Zong ^b   Zou, Quan ^a   Ji, Zhi Liang ^a  

^a XIAMEN UNIVERSITY   (China)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; MULTIFUNCTIONAL ENZYME; TETRAHYDROFOLIC ACID DERIVATIVE; UNCLASSIFIED DRUG;

ARCHAEON; ARTICLE; CATALYSIS; DATA BASE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME CONFORMATION; EUKARYOTE; GENE LOSS; HYDROPHOBICITY; PHYSICAL CHEMISTRY; SEQUENCE HOMOLOGY; SUPPORT VECTOR MACHINE;

DATABASES, PROTEIN; ENZYMES; MODELS, BIOLOGICAL; SUPPORT VECTOR MACHINES;

EID: 84862491711     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038979     Document Type: Article

References (41)

1. Carbonell P, Lecointre G, Faulon JL, (2011) Origins of specificity and promiscuity in metabolic networks. J Biol Chem 286: 43994-44004.
2. Jeffery CJ, (2003) Multifunctional proteins: examples of gene sharing. Ann Med 35: 28-35.
3. Jeffery CJ, (2003) Moonlighting proteins: old proteins learning new tricks. Trends Genet 19: 415-417.
4. Huberts DH, van der Klei IJ, (2010) Moonlighting proteins: an intriguing mode of multitasking. Biochim Biophys Acta 1803: 520-525.
5. Hult K, Berglund P, (2007) Enzyme promiscuity: mechanism and applications. Trends Biotechnol 25: 231-238.
6. Jensen RA, (1976) Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30: 409-425.
7. Copley SD, (2003) Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr Opin Chem Biol 7: 265-272.
8. Aharoni A, Gaidukov L, Khersonsky O, Gould SMcQ, Roodveldt C, et al. (2005) The 'evolvability' of promiscuous protein functions. Nat Genet 37: 73-76.
9. Jeffery CJ, (2004) Molecular mechanisms for multitasking: recent crystal structures of moonlighting proteins. Curr Opin Struct Biol 14: 663-668.
10. Canada KA, Iwashita S, Shim H, Wood TK, (2002) Directed evolution of toluene ortho-monooxygenase for enhanced 1-naphthol synthesis and chlorinated ethene degradation. J Bacteriol 184: 344-349.
11. Zheng W, Scheibner KA, Ho AK, Cole PA, (2001) Mechanistic studies on the alkyltransferase activity of serotonin N-acetyltransferase. Chem Biol 8: 379-389.
12. Gomez A, Domedel N, Cedano J, Pinol J, Querol E, (2003) Do current sequence analysis algorithms disclose multifunctional (moonlighting) proteins? Bioinformatics 19: 895-896.
13. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
14. Moore B, (2004) Bifunctional and moonlighting enzymes: lighting the way to regulatory control. Trends Plant Sci 9: 221-228.
15. Magrane M, Consortium U, (2011) UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011: bar009.
16. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Res 38: D211-222.
17. Cai CZ, Han LY, Ji ZL, Chen X, Chen YZ, (2003) SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res 31: 3692-3697.
18. Cherkassky V, (1997) The nature of statistical learning theory~. IEEE Trans Neural Netw 8: 1564.
19. Mohammad TA, Nagarajaram HA, (2011) Svm-based method for protein structural class prediction using secondary structural content and structural information of amino acids. J Bioinform Comput Biol 9: 489-502.
20. Jiang P, Wu H, Wang W, Ma W, Sun X, et al. (2007) MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res 35: W339-344.
21. Todd AE, Orengo CA, Thornton JM, (2002) Plasticity of enzyme active sites. Trends Biochem Sci 27: 419-426.
22. Ding CH, Dubchak I, (2001) Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 17: 349-358.
23. Lee HC, Graeff RM, Walseth TF, (1997) ADP-ribosyl cyclase and CD38. Multi-functional enzymes in Ca+2 signaling. Adv Exp Med Biol 419: 411-419.
24. Chen YH, Li MH, Zhang Y, He LL, Yamada Y, et al. (2004) Structural basis of the alpha1-beta subunit interaction of voltage-gated Ca2+ channels. Nature 429: 675-680.
25. Tochio H, Ohki S, Zhang Q, Li M, Zhang M, (1998) Solution structure of a protein inhibitor of neuronal nitric oxide synthase. Nat Struct Biol 5: 965-969.
26. Bairoch A, (2000) The ENZYME database in 2000. Nucleic Acids Res 28: 304-305.
27. Sakanyan V, Charlier D, Legrain C, Kochikyan A, Mett I, et al. (1993) Primary structure, partial purification and regulation of key enzymes of the acetyl cycle of arginine biosynthesis in Bacillus stearothermophilus: dual function of ornithine acetyltransferase. J Gen Microbiol 139: 393-402.
28. Elkins JM, Kershaw NJ, Schofield CJ, (2005) X-ray crystal structure of ornithine acetyltransferase from the clavulanic acid biosynthesis gene cluster. Biochem J 385: 565-573.
29. Timofeyeva NA, Koval VV, Knorre DG, Zharkov DO, Saparbaev MK, et al. (2009) Conformational dynamics of human AP endonuclease in base excision and nucleotide incision repair pathways. J Biomol Struct Dyn 26: 637-652.
30. Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res 36: D419-425.
31. Jeffery CJ, (2009) Moonlighting proteins-an update. Mol Biosyst 5: 345-350.
32. Marchot P, Chatonnet A, (2012) Enzymatic activity and protein interactions in alpha/beta hydrolase fold proteins: moonlighting versus promiscuity. Protein Pept Lett 19: 132-143.
33. Aoki-Kinoshita KF, Kanehisa M, (2007) Gene annotation and pathway mapping in KEGG. Methods Mol Biol 396: 71-91.
34. Peregrin-Alvarez JM, Sanford C, Parkinson J, (2009) The conservation and evolutionary modularity of metabolism. Genome Biol 10: R63.
35. Zientz E, Dandekar T, Gross R, (2004) Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiol Mol Biol Rev 68: 745-770.
36. Schmidt S, Sunyaev S, Bork P, Dandekar T, (2003) Metabolites: a helping hand for pathway evolution? Trends Biochem Sci 28: 336-341.
37. Genschel U, (2004) Coenzyme A biosynthesis: reconstruction of the pathway in archaea and an evolutionary scenario based on comparative genomics. Mol Biol Evol 21: 1242-1251.
38. Prasannan P, Appling DR, (2009) Human mitochondrial C1-tetrahydrofolate synthase: submitochondrial localization of the full-length enzyme and characterization of a short isoform. Arch Biochem Biophys 481: 86-93.
39. Prasannan P, Pike S, Peng K, Shane B, Appling DR, (2003) Human mitochondrial C1-tetrahydrofolate synthase: gene structure, tissue distribution of the mRNA, and immunolocalization in Chinese hamster ovary calls. J Biol Chem 278: 43178-43187.
40. Whitehead TR, Park M, Rabinowitz JC, (1988) Distribution of 10-formyltetrahydrofolate synthetase in eubacteria. J Bacteriol 170: 995-997.
41. Breitling R, Marijanovic Z, Perovic D, Adamski J, (2001) Evolution of 17beta-HSD type 4, a multifunctional protein of beta-oxidation. Mol Cell Endocrinol 171: 205-210.