Novel approach for structural identification of protein family: glyoxalase I

References

• Agarval, R., Almo, S. C., & Swaminathan, S. (2011). New York structural genomics consortium, RCSB Protein Data Bank, PDB code 3R4Q.
   Google Scholar
• Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389–3402.10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• Andreeva, A., Howorth, D., Brenner, S. E., Hubbard, T. J., Chothia, C., & Murzin, A. G. (2004). SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Reearch, 32, D226–D229.
   PubMed Web of Science ®Google Scholar
• Aronsson, A. C., Marmstal, E., & Mannervik, B. (1978). Glyoxalase I, a zinc metalloenzyme of mammals and yeast. Biochemical and Biophysical Research Communications, 81, 1235–1240.10.1016/0006-291X(78)91268-8
   PubMed Web of Science ®Google Scholar
• Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., … Bork, P. (2011). Enterotypes of the human gut microbiome. Nature, 473, 174–180.10.1038/nature09944
   PubMed Web of Science ®Google Scholar
• Ayoub, F. M., Allen, R. E., & Thornalley, P. J. (1993). Inhibition of proliferation of human leukemia 60 cells by methylglyoxal in vitro. Leukemia Research, 17, 397–401.10.1016/0145-2126(93)90094-2
   PubMed Web of Science ®Google Scholar
• Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2013). GenBank. Nucleic Acids Research, 41, 36–42. Retrieved from www.ncbi.nlm.nih.gov/genbank/
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28, 235–242. RCSB PDB. Retrieved from www.rcsb.org
   PubMed Web of Science ®Google Scholar
• Cameron, A. D., Olin, B., Ridderstrom, M., Mannervik, B., & Jones, T. A. (1997). Crystal structure of human glyoxalase I – Evidence for gene duplication and 3D domain swapping. The EMBO Journal, 16, 3386–3395.10.1093/emboj/16.12.3386
   PubMed Web of Science ®Google Scholar
• Chirgadze, Y. N., Boshkova, E. A., Battaile, K. P., Mendes, V. G., Lam, R., Chan, T. S. Y., … Chirgadze, N. Y. (2017). Crystal structure of Staphylococcus aureus Zn-glyoxalase I: New subfamily of glyoxalase I family. Journal of Biomolecular Structure and Dynamics, 35, 1–11. doi:10.1080/07391102.2016.1278038
   PubMedGoogle Scholar
• Chirgadze, Y. N., Nevskaya, N. A., Sergeev, N. A., & Fomenkova, N. P. (1987). Evolutionary conservatism of molecular strtructure of gamma-crystallins of vertebrates. Molekularnaya Biologia (USSR), 21, 110–117.
   Web of Science ®Google Scholar
• Chirgadze, Y., Nevskaya, N., Vernoslova, E., Nikonov, S., Sergeev, Y., Brazhnikov, E., … Urzhumtsev, A. (1991). Crystal structure of calf eye lens gamma-crystallin IIIb at 2.5 Å resolution: Its relation to function. Experimental Eye Research, 53, 295–304.10.1016/0014-4835(91)90233-5
   PubMed Web of Science ®Google Scholar
• Clugston, S. L., Barnard, J. F. J., Kinach, R., Miedema, D., Ruman, R., Daub, E., & Honek, J. F. (1998). Overproduction and characterization of a dimeric non-zinc glyoxalase I from Escherichia coli: Evidence for optimal activation by nickel ions. Biochemistry, 37, 8754–8763.10.1021/bi972791w
   PubMed Web of Science ®Google Scholar
• Dumas, P., Bergdoll, M., Cagnon, C., & Masson, J. M. (1994). Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering. EMBO Journal, 13, 2483–2492.
   PubMed Web of Science ®Google Scholar
• Fielding, A. J., Kovaleva, E. G., Farquhar, E. R., Lipscomb, J. D., & Que, L. (2011). A hyperactive cobalt-substituted extradiol-cleaving catechol dioxygenase. JBIC Journal of Biological Inorganic Chemistry, 16, 341–355.10.1007/s00775-010-0732-0
   PubMed Web of Science ®Google Scholar
• Grice, E. A., & Segre, J. A. (2012). The human microbiome: Our second genome. Annual Review of Genomics and Human Genetics, 13, 151–170.10.1146/annurev-genom-090711-163814
   PubMed Web of Science ®Google Scholar
• He, M. M., Clugston, S. L., Honek, J. F., & Matthews, B. W. (2000). Determination of the structure of Escherichia coli glyoxalase I suggests a structural basis for differential metal activation. Biochemistry, 39, 8719–8727.10.1021/bi000856g
   PubMed Web of Science ®Google Scholar
• He, P., & Moran, G. R. (2011). Structural and mechanistic comparisons of the metal-binding members of the vicinal oxygen chelate (VOC) superfamily. Journal of Inorganic Biochemistry, 105, 1259–1272.10.1016/j.jinorgbio.2011.06.006
   PubMed Web of Science ®Google Scholar
• McCarthy, A. A., Baker, H. M., Shewry, S. C., Patchett, M. L., & Baker, E. N. (2001). Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: A novel enzymatic function on an ancient metal binding scaffold. Structure, 9, 637–646.10.1016/S0969-2126(01)00622-0
   PubMed Web of Science ®Google Scholar
• Murzin, A. G., Brenner, S. E., Hubbard, T., & Chothia, C. (1995). SCOP: A structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology, 247, 536–540.
   PubMed Web of Science ®Google Scholar
• Nimrod, G., Schushan, M., Steinberg, D. M., & Ben-Tal, N. (2008). Detection of functionally important regions in ‘hypothetical proteins’ of known structure. Structure, 16, 1755–1763.10.1016/j.str.2008.10.017
   PubMed Web of Science ®Google Scholar
• Protein Standard BLAST: Basic Local Alignment Search Tool. (2016). National Center for Biotechnology Information, US National Library of Medicine. Retrieved from https://blast.ncbi.nlm.nih.gov/Blast.cgi
   Google Scholar
• Rao, K. M., Sauder, J. M., Burlley, S. K., & Swaminathan, S. (2007). NewYork SGX Research Center for Structural Genomics, RCSB Protein Data Bank, PDB code 2RBB.
   Google Scholar
• Santarius, T., Bignell, G. R., Greenman, C. D., Widaa, S., Chen, L., Mahoney, C. L., … Stratton, M. R. (2010). GLO1 – A novel amplified gene in human cancer. Genes, Chromosomes Cancer, 49, 711–725.10.1002/gcc.20784
   PubMed Web of Science ®Google Scholar
• Sellin, S., Eriksson, L. E. G., Aronsson, A. C., & Mannervik, B. (1983). Octahedral metal coordination in the active site of glyoxalase I as evidenced by the properties of Co(II)-glyoxalase I. Journal of Biological Chemistry, 258, 2091–2093.
   PubMed Web of Science ®Google Scholar
• Sellin, S., & Mannervik, B. (1984). Metal dissociation constants for glyoxalase I reconstituted with Zn2+, Co2+, Mn2+, and Mg2+. Journal of Biological Chemistry, 259, 11426–11429.
   PubMed Web of Science ®Google Scholar
• Sillitoe, I., Lewis, T. E., Cuff, A., Das, S., Ashford, P., Dawson, N. L., … Orengo, C. A. (2015). CATH: Comprehensive structural and functional annotations for genome sequences. Nucleic Acids Research, 43 (Database issue), D376–D381.
   PubMedGoogle Scholar
• Sucdeo, N., Glugston, S. L., Daub, E., & Honek, J. F. (2004). Distinct classes of glyoxalase I: Metal specificity of the Yersinia pestis, Pseudomonas aeruginosa and Neisseria meningitidis enzymes. Biochemistry Journal, 384, 11–117.
   Web of Science ®Google Scholar
• Suttisansanee, U., Lau, K., Lagishetty, S., Rao, K. N., Swaminathan, S., Sauder, J. M., … Honek, J. F. (2011). Structural variation in bacterial glyoxalase I enzymes: Investigation of the metalloenzyme glyoxalase I from Clostridium acetobutylicum. Journal of Biological Chemistry, 286, 38367–38374.10.1074/jbc.M111.251603
   PubMed Web of Science ®Google Scholar
• Thornalley, P. J. (1996). Pharmacology of methylglyoxal: Formation, modification of proteins and nucleic acids, and enzymatic detoxigfication – A role in pathogenesis and antiproliferative chemotherapy. General Pharmacology: The Vascular System, 27, 565–573.10.1016/0306-3623(95)02054-3
   PubMedGoogle Scholar
• Thornalley, P. J. (2003). Glyaxalase I – Structure, function and critical role in the enzymatic defence against glycation. Biochemical Society Transactions, 31, 1343–1348.10.1042/bst0311343
   PubMed Web of Science ®Google Scholar
• Vander Jagt, D. L. (1989). The glyoxalase system. In D. Dolphin, R. Poulson, & O. Avramovic (Eds.), Glutathione: Chemical, biochemical and medical aspects Part A (pp. 597–641). New York, NY: Wiley.
   Google Scholar
• Von Grotthuss, M., Plewczynski, D., Ginalski, K., Rychlewski, L., & Shakhnovich, E. I. (2006). PDB-UF: Database of predicted enzymatic functions for unannotated protein structures from structural genomics. BMC Bioinformatics, 7, 1–10.10.1186/1471-2105-7-53
   PubMed Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1996). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8, 127–134.
   Google Scholar
• Wishart, D. S., Jewison, T., Guo, A. C., Wilson, M., Knox, C., Liu, Y., … Scalbert, A. (2013). HMDB 3.0 – The Human Metabolome Database in 2013. Nucleic Acids Research, 41 (Database issue), D801–D807.
   PubMedGoogle Scholar
• Zhang, Z. (2003). Mechanistic studies on protein tyrosine phosphatases. Progress in Nucleic Acids Research and Molecular Biology, 73, 171–220.10.1016/S0079-6603(03)01006-7
   PubMed Web of Science ®Google Scholar