Computational and SAXS-based structure insights of pectin acetyl esterase (CtPae12B) of family 12 carbohydrate esterase from Clostridium thermocellum ATCC 27405

References

• Akinosho, H., Kelsey, Y., Dan, C., & Arthur, R. (2014). The emergence of Clostridium thermocellum as a high utility candidate for consolidated bioprocessing applications. Frontiers in Chemistry, 2, 66. https://doi.org/10.3389/fchem.2014.00066
   PubMed Web of Science ®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(17), 3389–3402. https://doi.org/10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1–3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
   Web of Science ®Google Scholar
• Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). W. H. Freeman; Section 1.3, Chemical Bonds in Biochemistry.
   Google Scholar
• Bolvig, P. U., Pauly, M., Orfila, C., Scheller, H. V., & Schnorr, K. (2003). Sequence Analysis and Characterisation of a Novel Pectin Acetyl Esterase from Bacillus subtilis. In A. J. G. Voragen, H. Schols, & R. Visser (Eds.), Advances in Pectin and Pectinase Research (pp. 315–330). Springer.
   Google Scholar
• Boyle, N. M. O., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 1–14. https://doi.org/10.1186/1758-2946-3-33
   PubMedGoogle Scholar
• Caffall, K. H., & Mohnen, D. (2009). The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohydrate Research, 344(14), 1879–1900. https://doi.org/10.1016/j.carres.2009.05.021
   PubMed Web of Science ®Google Scholar
• Chandrayan, P. (2018). Biological function(s) and application (s) of pectin and pectin degrading enzymes. Biosciences, Biotechnology Research Asia, 15(1), 87–100. https://doi.org/10.13005/bbra/2611
   Google Scholar
• Erickson, H. P. (2009). Size and shape of protein molecules at the nanometer level determined by sedimentation, gel filtration, and electron microscopy. Biological Procedures Online, 11, 32–51. https://doi.org/10.1007/s12575-009-9008-x
   PubMed Web of Science ®Google Scholar
• Fischer, H. D. O. N., Oliveira Neto, M. D., Napolitano, H. B., Polikarpov, I., & Craievich, A. F. (2010). Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale. Journal of Applied Crystallography, 43(1), 101–109. https://doi.org/10.1107/S0021889809043076
   Google Scholar
• Fournet, G., & Guinier, A. (1955). Small angle scattering of X-rays (C. B. Walker & Yudowitch, Trans.) (pp. 7–78). John Wiley and Sons.
   Google Scholar
• Franke, D., Petoukhov, M. V., Konarev, P. V., Panjkovich, A., Tuukkanen, A., Mertens, H. D. T., Kikhney, A. G., Hajizadeh, N. R., Franklin, J. M., Jeffries, C. M., & Svergun, D. I. (2017). ATSAS 2.8: A comprehensive data analysis suite for small-angle scattering from macromolecular solutions. Journal of Applied Crystallography, 50(Pt 4), 1212–1225. https://doi.org/10.1107/S1600576717007786
   PubMedGoogle Scholar
• Govind, K., Murthy, M. R. N., & Savithri, H. S. (2013). Chapter 692- Sobemovirus peptidase. Handbooks of Proteolytic Enzymes, 3, 3141–3148.
   Google Scholar
• Goyal, D., Kumar, K., Sharma, K., & Goyal, A. (2020). Small-angle X-ray scattering based structure, modeling and molecular dynamics analyses of a family 5 glycoside hydrolase first endo-mannanase named as RfGH5_7 from Ruminococcus flavefaciens. Journal of Biomolecular Structure & Dynamics, 38(15), 4371–4384. https://doi.org/10.1080/07391102.2019.1680438
   PubMed Web of Science ®Google Scholar
• Hess, B., Kutzner, C., Spoel, D. V., & Lindahl, E. (2008). GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. https://doi.org/10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Hugouvieux-Cotte-Pattat, N., Condemine, G., & Shevchik, V. E. (2014). Bacterial pectate lyases, structural and functional diversity. Environmental Microbiology Reports, 6(5), 427–440. https://doi.org/10.1111/1758-2229.12166
   PubMed Web of Science ®Google Scholar
• Jing, X., Zeng, H., Wang, S., & Xu, J. (2020). A web-based protocol for interprotein contact prediction by deep learning. Methods in Molecular Biology (Clifton, N.J.), 2074, 67–80. https://doi.org/10.1007/978-1-4939-9873-9_6
   PubMedGoogle Scholar
• Jones, D. T. (1999). Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology, 292(2), 195–202. https://doi.org/10.1006/jmbi.1999.3091
   PubMed Web of Science ®Google Scholar
• Kamal, M. Z., Mohammad, T. A., Krishnamoorthy, G., & Rao, N. M. (2012). Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant. PloS One, 7(4), e35188. https://doi.org/10.1371/journal.pone.0035188
   PubMed Web of Science ®Google Scholar
• Kelly, S. M., Jess, T. J., & Price, N. C. (2005). How to study proteins by circular dichroism? Biochimica et Biophysica Acta, 1751(2), 119–139. https://doi.org/10.1016/j.bbapap.2005.06.005
   PubMed Web of Science ®Google Scholar
• Klausen, M. S., Jespersen, M. C., Nielsen, H., Jensen, K. K., Jurtz, V. I., Sønderby, C. K., Sommer, M. O. A., Winther, O., Nielsen, M., Petersen, B., & Marcatili, P. (2019). NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning. Proteins, 87(6), 520–527. https://doi.org/10.1002/prot.25674
   PubMed Web of Science ®Google Scholar
• Klose, D. P., Wallace, B. A., & Janes, R. W. (2010). 2Struc: The secondary structure server. Bioinformatics (Oxford, England), 26(20), 2624–2625. https://doi.org/10.1093/bioinformatics/btq480
   PubMed Web of Science ®Google Scholar
• Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H., & Svergun, D. I. (2003). PRIMUS: A Windows PC-based system for small-angle scattering data analysis. Journal of Applied Crystallography, 36(5), 1277–1282. https://doi.org/10.1107/S0021889803012779
   Web of Science ®Google Scholar
• Kozin, M. B., & Svergun, D. I. (2001). Automated matching of high-and low-resolution structural models. Journal of Applied Crystallography, 34(1), 33–41. https://doi.org/10.1107/S0021889800014126
   Google Scholar
• Krieger, E., Joo, K., Lee, J., Lee, J., Raman, S., Thompson, J., Tyka, M., Baker, D., & Karplus, K. (2009). Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins: Structure, Function, and Bioinformatics, 77(S9), 114–122. https://doi.org/10.1002/prot.22570
   PubMed Web of Science ®Google Scholar
• Kumar, K., Singh, S., Sharma, K., & Goyal, A. (2021). Computational modeling and small-angle X-ray scattering based structure analysis and identifying ligand cleavage mechanism by processive endocellulase of family 9 glycoside hydrolase (HtGH9) from Hungateiclostridium thermocellum ATCC 27405. Journal of Molecular Graphics & Modelling, 103, 107808. https://doi.org/10.1016/j.jmgm.2020.107808
   PubMed Web of Science ®Google Scholar
• Laddomada, F., Miyachiro, M. M., Jessop, M., Patin, D., Job, V., Mengin-Lecreulx, D., Le Roy, A., Ebel, C., Breyton, C., Gutsche, I., & Dessen, A. (2019). The MurG glycosyltransferase provides an oligomeric scaffold for the cytoplasmic steps of peptidoglycan biosynthesis in the human pathogen Bordetella pertussis. Scientific Reports, 9(1), 1–17. https://doi.org/10.1038/s41598-019-40966-z
   PubMedGoogle Scholar
• Lagaert, S., Beliën, T., & Volckaert, G. (2009). Plant cell walls: Protecting the barrier from degradation by microbial enzymes. Seminars in Cell & Developmental Biology, 20(9), 1064–1073. https://doi.org/10.1016/j.semcdb.2009.05.008
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., & Swindells, M. B. (2011). LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. Journal of Chemical Information and Modeling, 51(10), 2778–2786. https://doi.org/10.1021/ci200227u
   PubMed Web of Science ®Google Scholar
• Lau, E. Y., & Bruice, T. C. (1999). Consequences of breaking the Asp-His hydrogen bond of the catalytic triad: Effects on the structure and dynamics of the serine esterase cutinase. Biophysical Journal, 77(1), 85–98. https://doi.org/10.1016/S0006-3495(99)76874-8
   PubMed Web of Science ®Google Scholar
• Lovell, S. C., Davis, I. W., Arendall, I. I W. B., Bakker, P. I. W., Word, J. M., Prisant, M. G., Richardson, J. S., & Richardson, D. C. (2003). Structure validation by Cα geometry: φ/ψ and Cβ deviation. Proteins: Structure, Function, and Bioinformatics, 50(3), 437–450. https://doi.org/10.1002/prot.10286
   PubMed Web of Science ®Google Scholar
• Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D., & Lopez, R. (2019). The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Research, 47(W1), W636–W641. https://doi.org/10.1093/nar/gkz268
   PubMed Web of Science ®Google Scholar
• Matsunaga, T., Ishii, T., Matsumoto, S., Higuchi, M., Darvill, A., Albersheim, P., & O'Neill, M. A. (2004). Occurrence of the primary cell wall polysaccharide rhamnogalacturonan II in pteridophytes, lycophytes, and bryophytes. Implications for the evolution of vascular plants. Plant Physiology, 134(1), 339–351. https://doi.org/10.1104/pp.103.030072
   PubMed Web of Science ®Google Scholar
• Mohnen, D., Bar-Peled, M., & Somerville, C. (2008). Biosynthesis of plant cell walls. In M.Himmel (Ed.), Biomass Recalcitrance (pp. 94–187). Blackwell Publishing.
   Google Scholar
• Mølgaard, A., Kauppinen, S., & Larsen, S. (2000). Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases. Structure (London, England: 1993), 8(4), 373–383. https://doi.org/10.1016/s0969-2126(00)00118-0
   PubMed Web of Science ®Google Scholar
• Morgat, A., Lombardot, T., Coudert, E., Axelsen, K., Neto, T. B., Gehant, S., Bansal, P., Bolleman, J., Gasteiger, E., Castro, E., Baratin, D., Pozzato, M., Xenarios, I., Poux, S., Redaschi, N., & Bridge, A. (2020). The UniProt consortium, enzyme annotation in UniProtKB using Rhea. Bioinformatics, 36(6), 1896–1901.
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Morris, G. A., Kök, M. S., Harding, S. E., & Adams, G. A. (2010). Polysaccharide drug delivery systems based on pectin and chitosan. Biotechnology & Genetic Engineering Reviews, 27, 257–284. https://doi.org/10.1080/02648725.2010.10648153
   PubMed Web of Science ®Google Scholar
• Nath, P., Sharma, K., Kumar, K., & Goyal, A. (2020). Combined SAXS and computational approaches for structure determination and binding characteristics of Chimera (CtGH1-L1-CtGH5-F194A) generated by assembling β-glucosidase (CtGH1) and a mutant endoglucanase (CtGH5-F194A) from Clostridium thermocellum. International Journal of Biological Macromolecules, 148, 364–377. https://doi.org/10.1016/j.ijbiomac.2020.01.116
   PubMed Web of Science ®Google Scholar
• Ollis, D. L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Franken, S. M., Harel, M., Remington, S. J., Silman, I., & Schrag, J. (1992). The alpha/beta hydrolase fold . Protein Engineering, 5(3), 197–211. https://doi.org/10.1093/protein/5.3.197
   PubMedGoogle Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Polgar, L. (2005). The catalytic triad of serine peptidases. Cellular and Molecular Life Sciences, 62, 2161–2172.
   PubMed Web of Science ®Google Scholar
• Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42(Web Server issue), W320–W324. https://doi.org/10.1093/nar/gku316
   PubMed Web of Science ®Google Scholar
• Schrödinger, L. (2017). The PyMOL molecular graphics system, Version 2.0. http://www.pymol.org/
   Google Scholar
• Searle-van Leeuwen, M. J. F., van den Broek, L. A. M., Schols, H. A., Beldman, G., & Voragen, A. G. J. (1992). Rhamnogalacturonan acetylesterase: A novel enzyme from Aspergillus aculeatus, specific for the deacetylation of hairy regions of pectins. Applied Microbiology and Biotechnology, 38(3), 347–349. https://doi.org/10.1007/BF00170084
   Web of Science ®Google Scholar
• Sharma, K., Antunes, I. L., Rajulapati, V., & Goyal, A. (2018). Low-resolution SAXS and comparative modeling based structure analysis of endo-β-1,4-xylanase a family 10 glycoside hydrolase from Pseudopedobacter saltans comb. nov. International Journal of Biological Macromolecules, 112, 1104–1114. https://doi.org/10.1016/j.ijbiomac.2018.02.037
   PubMed Web of Science ®Google Scholar
• Shevchik, V., & Hugouvieux-Cotte-Pattat, N. (2003). PaeX, a second pectin acetylesterase of Erwinia chrysanthemi 3937. Journal of Bacteriology, 185(10), 3091–3100. https://doi.org/10.1128/jb.185.10.3091-3100.2003
   PubMed Web of Science ®Google Scholar
• Söderberg, C. A., Månsson, C., Bernfur, K., Rutsdottir, G., Härmark, J., Rajan, S., Al-Karadaghi, S., Rasmussen, M., Höjrup, P., Hebert, H., & Emanuelsson, C. (2018). Structural modelling of the DNAJB6 oligomeric chaperone shows a peptide-binding cleft lined with conserved S/T-residues at the dimer interface. Scientific Reports, 8(1), 1–15. https://doi.org/10.1038/s41598-018-23035-9
   PubMedGoogle Scholar
• Svergun, D. I. (1992). Determination of the regularization parameter in indirect-transform methods using perceptual criteria. Journal of Applied Crystallography, 25(4), 495–503. https://doi.org/10.1107/S0021889892001663
   Web of Science ®Google Scholar
• Tian, W., Chen, C., Lei, X., Zhao, J., & Liang, J. (2018). CASTp 3.0: Computed atlas of surface topography of proteins. Nucleic Acids Research, 46(W1), W363–W367. https://doi.org/10.1093/nar/gky473
   PubMed Web of Science ®Google Scholar
• Volkov, V. V., and., & Svergun, D. I. (2003). Uniqueness of ab initio shape determination in small angle scattering. Journal of Applied Crystallography, 36(3), 860–864. https://doi.org/10.1107/S0021889803000268
   Google Scholar
• Voragen, A., Coenen Gerd-Jan, G. J., Verhoef, R. P., & Schols, H. A. (2009). Pectin, a versatile polysaccharide present in plant cell walls. Structural Chemistry, 20(2), 263–275. https://doi.org/10.1007/s11224-009-9442-z
   Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–W410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Xu, Y., & Meng, X. (2020). Molecular Simulation Elaborating the Mechanism of 1β-Hydroxy Alantolactone Inhibiting Ubiquitin-Conjugating Enzyme UbcH5s. Scientific Reports, 10(1), 141. https://doi.org/10.1038/s41598-019-57104-4
   PubMed Web of Science ®Google Scholar
• Svergun, D. I. B. C. K. M. H. J., Barberato, C., & Koch, M. H. (1995). CRYSOL–a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. Journal of Applied Crystallography, 28(6), 768–773. https://doi.org/10.1107/S0021889895007047
   Web of Science ®Google Scholar
• Yang, J., & Zhang, Y. (2015). I-TASSER server: New development for protein structure and function predictions. Nucleic Acids Research, 43(W1), W174–W181. https://doi.org/10.1093/nar/gkv342
   PubMed Web of Science ®Google Scholar
• Yang, J., Wang, Y., & Zhang, Y. (2016). ResQ: An approach to unified estimation of B-factor and residue-specific error in protein structure prediction. Journal of Molecular Biology, 428(4), 693–701. https://doi.org/10.1016/j.jmb.2015.09.024
   PubMed Web of Science ®Google Scholar
• Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9, 40. https://doi.org/10.1186/1471-2105-9-40
   PubMed Web of Science ®Google Scholar
• Zverlov, V. V., Schantz, N., Schmitt-Kopplin, P., & Schwarz, W. H. (2005). Two new major subunits in the cellulosome of Clostridium thermocellum: Xyloglucanase Xgh74A and endoxylanase Xyn10D. Microbiology (Reading, England), 151(Pt 10), 3395–3401. https://doi.org/10.1099/mic.0.28206-0
   PubMedGoogle Scholar