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Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution

By Marina V Omelchenko, Michael Y Galperin, Yuri I Wolf and Eugene V Koonin
Topics: Research
Publisher: BioMed Central
OAI identifier: oai:pubmedcentral.nih.gov:2876114
Provided by: PubMed Central

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  1. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol
  2. (2001). A: Archaeal shikimate kinase, a new member of the GHMP-kinase family.
  3. (2010). A: MEROPS: the peptidase database. Nucleic Acids Res
  4. (2008). A: The Pfam protein families database. Nucleic Acids Res
  5. (1996). Affinity purification and comparative analysis of two distinct human uracilDNA glycosylases. Exp Cell Res
  6. (2008). AG: Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res
  7. (2006). AG: House cleaning, a part of good housekeeping. Mol Microbiol
  8. (2009). AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res
  9. (1998). Analogous enzymes: independent inventions in enzyme evolution. Genome Res
  10. (2008). AnEnPi: identification and annotation of analogous enzymes.
  11. (2007). Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Res
  12. (1997). Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi. Proc Natl Acad Sci USA
  13. (2009). Beliaev AS: Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. Proc Natl Acad Sci USA
  14. (1976). Bisswanger H: Multifunctional proteins. Annu Rev Biochem
  15. (2004). Call for an enzyme genomics initiative. Genome Biol
  16. (2005). Chromosome alignment and segregation regulated by ubiquitination of survivin. Science
  17. (2008). CL: Moonlighting proteins in yeasts. Microbiol Mol Biol Rev
  18. (2004). Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions.
  19. Concepts of molecular biosemiotics and of molecular evolution.
  20. (2004). Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res
  21. (1994). Convergent evolution: the need to be explicit. Trends Biochem Sci
  22. (2009). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res
  23. (1975). DC: Crystal structure of bovine Cu, Zn superoxide dismutase at 3 A resolution: chain tracing and metal ligands. Proc Natl Acad Sci USA
  24. (1970). Distinguishing homologous from analogous proteins. Syst Zool
  25. (2004). Djinovic Carugo K: Crystal structure of nickel-containing superoxide dismutase reveals another type of active site. Proc Natl Acad Sci USA
  26. (2009). E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics
  27. (2003). E: Scaling laws in the functional content of genomes. Trends Genet
  28. (1976). Enzyme recruitment in evolution of new function. Annu Rev Microbiol
  29. (2003). Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res
  30. (2003). Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr Opin Chem Biol
  31. (2003). Evolution and classification of P-loop kinases and related proteins.
  32. (1977). Evolution and tinkering. Science
  33. Evolution of metabolic pathways in enteric bacteria. In Escherichia coli and Salmonella: cellular and molecular biology Edited by: Neidhardt FC, Curtiss III
  34. (1999). Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes. Genetica
  35. (2008). Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res
  36. (2007). Gerlt JA: Evolutionary potential of b/a8-barrels: stepwise evolution of a "new" reaction in the enolase superfamily. Biochemistry
  37. (2007). Glycerate kinase of the hyperthermophilic archaeon Thermoproteus tenax: new insights into the phylogenetic distribution and physiological role of members of the three different glycerate kinase classes. BMC Genomics
  38. (2009). Godzik A: Threedimensional structural view of the central metabolic network of Thermotoga maritima. Science
  39. (2009). Grishin NV: Discrete-continuous duality of protein structure space. Curr Opin Struct Biol
  40. (1998). JA: Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry
  41. (2007). JB: Using reaction mechanism to measure enzyme similarity.
  42. (2009). JM: Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics
  43. (2002). Karp PD: Evaluation of computational metabolic-pathway predictions for Helicobacter pylori. Bioinformatics
  44. (2008). KEGG for linking genomes to life and the environment. Nucleic Acids Res
  45. (2010). Klei IJ van der: Moonlighting proteins: An intriguing mode of multitasking. Biochim Biophys Acta
  46. (2005). Lercher MJ: Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet
  47. (2009). Lessons from structural genomics. Annu Rev Biophys
  48. (1997). Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res
  49. (2010). Lupas AN, Söding J: A galaxy of folds. Protein Sci
  50. (1983). ML: Iron superoxide dismutase from Escherichia coli at 3.1-Å resolution: a structure unlike that of copper/zinc protein at both monomer and dimer levels. Proc Natl Acad Sci USA
  51. (2009). Moonlighting proteins--an update. Mol BioSyst
  52. (1999). Moonlighting proteins. Trends Biochem Sci
  53. (1999). MW: Molecular basis of glutathione synthetase deficiency and a rare gene permutation event.
  54. (2001). Novel type of glucose-6-phosphate isomerase in the hyperthermophilic archaeon Pyrococcus furiosus.
  55. (2002). One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
  56. (2009). Orengo CA: The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res
  57. (2007). Rawlings ND: 'Species' of peptidases.
  58. (2005). Rayment I: Divergent evolution in the enolase superfamily: the interplay of mechanism and specificity. Arch Biochem Biophys
  59. (1992). Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes by the Reactions they Catalyse.
  60. (1986). Relationships of human protein sequences to those of other organisms. Cold Spring Harbor Symp Quant Biol
  61. (1961). Report of the Commission on Enzymes of the International Union of Biochemistry.
  62. (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions.
  63. (2002). Sequence - Evolution - Function. Computational Approaches in Comparative Genomics.
  64. (1991). Sirover MA: A human nuclear uracil DNA glycosylase is the 37-kDa subunit of glyceraldehyde-3-phosphate dehydrogenase. Proc Natl Acad Sci USA
  65. (1997). Söll D: A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science
  66. (2004). Strimmer K: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics.
  67. (2009). Structure and mechanism of a eukaryotic FMN adenylyltransferase.
  68. (2009). SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res
  69. (2005). Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics
  70. (2003). Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol
  71. (2000). The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res
  72. (2000). The ENZYME database in 2000. Nucleic Acids Res
  73. (2006). The impact of structural genomics: expectations and outcomes. Science
  74. (2001). The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus is a unique glycolytic enzyme that belongs to the cupin superfamily. J Biol Chem
  75. (2001). The TIM-barrel fold: a versatile framework for efficient enzymes.
  76. (2009). The UniProt Consortium: The Universal Protein Resource (UniProt)
  77. (2000). Thornburg RW: Tobacco nectarin I. Purification and characterization as a germin-like, manganese superoxide dismutase implicated in the defense of floral reproductive tissues.
  78. (2004). TJ: Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins.
  79. (1991). TR: Drosophila melanogaster diphenol oxidase A2: gene structure and homology with the mouse mast-cell tumtransplantation antigen, P91A. Gene
  80. (2009). van Nimwegen E: Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends Genet
  81. (2005). Yakunin AF: Enzyme genomics: Application of general enzymatic screens to discover new enzymes. FEMS Microbiol Rev