Functional identification of ‘hypothetical protein’ structures with unknown function

References

• Altschul, S. F., Madden, T. L., Schaffer, 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(17), 3389–3402. https://doi.org/10.1093/nar/25.17.3389
   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 Res, 41, 36–42.
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D., & Zardecki, C. (2002). The Protein Data Bank. Acta Crystallographica. Section D, Biological Crystallography, 58 (Pt 6 No 1), 899–907. https://doi.org/10.1107/s0907444902003451
   PubMedGoogle 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(12), 3386–3395.
   PubMed Web of Science ®Google Scholar
• Chirgadze, Y. (1987). Deduction and systematic classification of spatial motifs of the antiparallel β-structure in globular proteins. Acta Cryst, A43, 405–417.
   Google Scholar
• Chirgadze, Y. N., Boshkova, E. A., Battaile, K. P., Mendes, V. G., Lam, R., Chan, T. S. Y., Romanov, V., Pai, E. F., & Chirgadze, N. Y. (2018). Crystal structure of Staphylococcus aureus Zn-glyoxalase I: New subfamily of glyoxalase I family. Journal of Biomolecular Structure and Dynamics, 36(2), 376–386. https://doi.org/10.1080/07391102.2016.1278038
   PubMed Web of Science ®Google Scholar
• Chirgadze, Y. N., Clarke, T. E., Romanov, V., Kisselman, G., Wu-Brown, J., Soloveychik, M., Chan, T. S. Y., Gordon, R. D., Battaile, K. P., Pai, E. F., & Chirgadze, N. Y. (2015). The structure of SAV1646 from Staphylococcus aureus belonging to a new ‘ribosome-associated’ subfamily of bacterial proteins. Acta Crystallographica Section D: Biological Crystallography, D71, 332–337.
   Google Scholar
• Clarke, T. E., Romanov, V., Chirgadze, Y. N., Klomsiri, C., Kisselman, G., Wu-Brown, J., Poole, L. B., Pai, E. F., & Chirgadze, N. Y. (2011). Crystal structure of alkyl hydroperoxidase D like protein PA0269 from Pseudomonas aeruginosa: Homology of the AhpD-like structural family. BMC Structural Biology, 11, 27. https://doi.org/10.1186/1472-6807-11-27
   PubMed Web of Science ®Google Scholar
• Das, S., & Orengo, C. A. (2016). Protein function annotation using protein domain family resources. Methods (San Diego, California), 93, 24–34. https://doi.org/10.1016/j.ymeth.2015.09.029
   PubMed Web of Science ®Google Scholar
• Efimov, A. V. (1993). Standard structures in proteins. Progress in Biophysics and Molecular Biology, 60(3), 201–239. https://doi.org/10.1016/0079-6107(93)90015-C
   PubMed Web of Science ®Google Scholar
• Efimov, A. V. (1997). Structural trees for protein superfamilies. Proteins: Structure, Function, and Genetics, 28(2), 241–261. https://doi.org/10.1002/(SICI)1097-0134(199706)28:2<241::AID-PROT12>3.0.CO;2-I
   PubMed Web of Science ®Google Scholar
• Gordeev, A. B., Kargatov, A. M., & Efimov, A. V. (2010). PCBOST: Protein classification based on structural trees. Biochemical and Biophysical Research Communications, 397(3), 470–471. https://doi.org/10.1016/j.bbrc.2010.05.136
   PubMed Web of Science ®Google Scholar
• Gordon, R. D., Qiu, W., Romanov, V., Lam, K., Soloveychik, M., Benetteraj, D., Battaile, K., Chirgadze Yu, N., Pai, E., & Chirgadze, N. Y. (2013). Crystal structure of the CN-hydrolase SA0302 from the pathogenic bacterium Staphylococcus aureus belonging to the Nit and NitFhit Branch of the nitrilase superfamily. Journal of Biomolecular Structure & Dynamics, 31(10), 1057–1065. https://doi.org/10.1080/07391102.2012.719111
   PubMed Web of Science ®Google Scholar
• 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, 53.
   PubMed Web of Science ®Google Scholar
• Hattori, M., Mizohata, E., Manzoku, M., Bessho, Y., Murayama, K., Terada, K., Kuramitsu, S., Shirouzu, M., & Yokoyama, S. (2005). Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8. Proteins, 61(4), 1117–1120. https://doi.org/10.1002/prot.20692
   PubMed Web of Science ®Google Scholar
• Kargatov, A. M., Boshkova, E. A., & Chirgadze, Y. N. (2018). Novel approach for structural identification of protein family: Glyoxalase I. Journal of Biomolecular Structure & Dynamics, 36(10), 2699–2712. https://doi.org/10.1080/07391102.2017.1367330
   PubMed Web of Science ®Google Scholar
• Mizohata, E., Hattori, M., Kuramitsu, S., Shirouzu, M., & Yokoyama, S. (2005). Crystal structure of hypothetical protein TTHA1013 from an extremely thermophilic bacterium Thermus thermophilus HB8. The Protein Data Bank, PDB ID 1wv8. https://doi.org/10.2210/pdb1wv8/pdb
   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(4), 536–540.
   PubMed Web of Science ®Google Scholar