Rossmann-Fold Methyltransferases: Taking a "β-Turn" around Their Cofactor, S-Adenosylmethionine

Biochemistry

Volumn 58, Issue 3, 2019, Pages 166-170

  Chouhan, Bhanu Pratap Singh ^a   Maimaiti, Shayida ^a   Gade, Madhuri ^a   Laurino, Paola ^a  

^a OKINAWA INSTITUTE OF SCIENCE AND TECHNOLOGY GRADUATE UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACIDS; NUCLEOTIDES;

ACIDIC RESIDUES; COFACTOR BINDING; FLAVIN ADENINE DINUCLEOTIDE; METHYLTRANSFERASES; NICOTINAMIDE ADENINE DINUCLEOTIDES; S-ADENOSYLMETHIONINE; STRUCTURAL CONFORMATIONS; STRUCTURAL FEATURE;

ENZYMES;

ALANINE; DNA METHYLTRANSFERASE; GLYCINE; METHIONINE; METHYLTRANSFERASE; NITROGEN; OXYGEN; S ADENOSYLMETHIONINE; FLAVINE ADENINE NUCLEOTIDE; NICOTINAMIDE ADENINE DINUCLEOTIDE;

ALPHA HELIX; ARTICLE; BETA TURN; BIOINFORMATICS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME STABILITY; HYDROGEN BOND; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; RESIDUE ANALYSIS; SITE DIRECTED MUTAGENESIS; STRUCTURE ANALYSIS; BINDING SITE; CHEMISTRY; COENZYME; COMPUTER SIMULATION; GENETICS; METABOLISM; METHYLATION; MUTAGENESIS;

ALANINE; BINDING SITES; COENZYMES; COMPUTER SIMULATION; FLAVIN-ADENINE DINUCLEOTIDE; GLYCINE; METHYLATION; METHYLTRANSFERASES; MUTAGENESIS; NAD; PROTEIN CONFORMATION; PROTEIN FOLDING; S-ADENOSYLMETHIONINE;

EID: 85056903897     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.8b00994     Document Type: Article

References (32)

1. Schubert, H. L., Blumenthal, R. M., and Cheng, X. (2003) Many paths to methyltransfer: a chronicle of convergence. Trends Biochem. Sci. 28, 329-335, 10.1016/S0968-0004(03)00090-2
2. Struck, A. W., Thompson, M. L., Wong, L. S., and Micklefield, J. (2012) S-adenosyl-methionine-dependent methyltransferases: highly versatile enzymes in biocatalysis, biosynthesis and other biotechnological applications. ChemBioChem 13, 2642-2655, 10.1002/cbic.201200556
3. Rao, S. T. and Rossmann, M. G. (1973) Comparison of super-secondary structures in proteins. J. Mol. Biol. 76, 241-256, 10.1016/0022-2836(73)90388-4
4. Aravind, L., Mazumder, R., Vasudevan, S., and Koonin, E. V. (2002) Trends in protein evolution inferred from sequence and structure analysis. Curr. Opin. Struct. Biol. 12, 392-399, 10.1016/S0959-440X(02)00334-2
5. Xie, L. and Bourne, P. E. (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc. Natl. Acad. Sci. U. S. A. 105, 5441-5446, 10.1073/pnas.0704422105
6. Edwards, H., Abeln, S., and Deane, C. M. (2013) Exploring fold space preferences of new-born and ancient protein superfamilies. PLoS Comput. Biol. 9, e1003325, 10.1371/journal.pcbi.1003325
7. Bukhari, S. A. and Caetano-Anolles, G. (2013) Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes. PLoS Comput. Biol. 9, e1003009, 10.1371/journal.pcbi.1003009
8. Caetano-Anolles, G. and Caetano-Anolles, D. (2003) An evolutionarily structured universe of protein architecture. Genome Res. 13, 1563-1571, 10.1101/gr.1161903
9. Caetano-Anolles, G. and Caetano-Anolles, D. (2005) Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J. Mol. Evol. 60, 484-498, 10.1007/s00239-004-0221-6
10. Rossmann, M. G., Moras, D., and Olsen, K. W. (1974) Chemical and biological evolution of nucleotide-binding protein. Nature 250, 194-199, 10.1038/250194a0
11. Caetano-Anolles, G., Kim, H. S., and Mittenthal, J. E. (2007) The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture. Proc. Natl. Acad. Sci. U. S. A. 104, 9358-9363, 10.1073/pnas.0701214104
12. Ma, B. G., Chen, L., Ji, H. F., Chen, Z. H., Yang, F. R., Wang, L., Qu, G., Jiang, Y. Y., Ji, C., and Zhang, H. Y. (2008) Characters of very ancient proteins. Biochem. Biophys. Res. Commun. 366, 607-611, 10.1016/j.bbrc.2007.12.014
13. Nath, N., Mitchell, J. B., and Caetano-Anolles, G. (2014) The natural history of biocatalytic mechanisms. PLoS Comput. Biol. 10, e1003642, 10.1371/journal.pcbi.1003642
14. Kim, K. M. and Caetano-Anolles, G. (2011) The proteomic complexity and rise of the primordial ancestor of diversified life. BMC Evol. Biol. 11, 140, 10.1186/1471-2148-11-140
15. Gherardini, P. F., Wass, M. N., Helmer-Citterich, M., and Sternberg, M. J. (2007) Convergent evolution of enzyme active sites is not a rare phenomenon. J. Mol. Biol. 372, 817-845, 10.1016/j.jmb.2007.06.017
16. Cheng, H., Schaeffer, R. D., Liao, Y., Kinch, L. N., Pei, J., Shi, S., Kim, B. H., and Grishin, N. V. (2014) ECOD: an evolutionary classification of protein domains. PLoS Comput. Biol. 10, e1003926, 10.1371/journal.pcbi.1003926
17. Efimov, A. V. (1997) Structural trees for protein superfamilies. Proteins: Struct., Funct., Genet. 28, 241-260, 10.1002/(SICI)1097-0134(199706)28:2<241::AID-PROT12>3.0.CO;2-I
18. Panchenko, A. R. and Madej, T. (2004) Analysis of protein homology by assessing the (dis)similarity in protein loop regions. Proteins: Struct., Funct., Genet. 57, 539-547, 10.1002/prot.20237
19. Bujnicki, J. M. (1999) Comparison of protein structures reveals monophyletic origin of the AdoMet-dependent methyltransferase family and mechanistic convergence rather than recent differentiation of N4-cytosine and N6-adenine DNA methylation. In Silico Biol. 1, 175-182
20. Wierenga, R. K., Terpstra, P., and Hol, W. G. (1986) Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint. J. Mol. Biol. 187, 101-107, 10.1016/0022-2836(86)90409-2
21. Dym, O. and Eisenberg, D. (2001) Sequence-structure analysis of FAD-containing proteins. Protein Sci. 10, 1712-1728, 10.1110/ps.12801
22. Lupas, A. N., Ponting, C. P., and Russell, R. B. (2001) On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?. J. Struct. Biol. 134, 191-203, 10.1006/jsbi.2001.4393
23. Gana, R., Rao, S., Huang, H., Wu, C., and Vasudevan, S. (2013) Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach. BMC Struct. Biol. 13, 6, 10.1186/1472-6807-13-6
24. Kozbial, P. Z. and Mushegian, A. R. (2005) Natural history of S-adenosylmethionine-binding proteins. BMC Struct. Biol. 5, 19, 10.1186/1472-6807-5-19
25. Laurino, P., Toth-Petroczy, A., Meana-Paneda, R., Lin, W., Truhlar, D. G., and Tawfik, D. S. (2016) An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors. PLoS Biol. 14, e1002396, 10.1371/journal.pbio.1002396
26. Hutchinson, E. G. and Thornton, J. M. (1994) A revised set of potentials for beta-turn formation in proteins. Protein Sci. 3, 2207-2216, 10.1002/pro.5560031206
27. Hutchinson, E. G. and Thornton, J. M. (1996) PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci. 5, 212-220, 10.1002/pro.5560050204
28. Crooks, G. E., Hon, G., Chandonia, J. M., and Brenner, S. E. (2004) WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190, 10.1101/gr.849004
29. Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., and Serrano, L. (2005) The FoldX web server: an online force field. Nucleic Acids Res. 33, W382-388, 10.1093/nar/gki387
30. Rockah-Shmuel, L. and Tawfik, D. S. (2012) Evolutionary transitions to new DNA methyltransferases through target site expansion and shrinkage. Nucleic Acids Res. 40, 11627-11637, 10.1093/nar/gks944
31. Jacquet, P., Hiblot, J., Daude, D., Bergonzi, C., Gotthard, G., Armstrong, N., Chabriere, E., and Elias, M. (2017) Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase. Sci. Rep. 7, 16745, 10.1038/s41598-017-16841-0
32. Murphy, P. M., Bolduc, J. M., Gallaher, J. L., Stoddard, B. L., and Baker, D. (2009) Alteration of enzyme specificity by computational loop remodeling and design. Proc. Natl. Acad. Sci. U. S. A. 106, 9215-9220, 10.1073/pnas.0811070106