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

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dc.contributor.author Kumar, Krishan
dc.contributor.author Singh, Shubha
dc.contributor.author Sharma, Kedar
dc.contributor.author Goyal, Arun
dc.date.accessioned 2020-12-02T15:27:05Z
dc.date.available 2020-12-02T15:27:05Z
dc.date.issued 2021-03
dc.identifier.citation Kumar, Krishan; Singh, Shubha; Sharma, Kedar and Goyal, Arun, “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 and Modelling, DOI: 10.1016/j.jmgm.2020.107808, vol. 103, Mar. 2021. en_US
dc.identifier.issn 1093-3263
dc.identifier.uri https://doi.org/10.1016/j.jmgm.2020.107808
dc.identifier.uri https://repository.iitgn.ac.in/handle/123456789/5907
dc.description.abstract The cellulases of family 9 glycoside hydrolase with subtle difference in amino acid sequence have shown different types of catalytic activities such as endo-, exo- or processive endocellulase. However, the reason behind the different types of catalytic activities still unclear. In this study, the processive endocellulase, HtGH9 of family 9 GH from Hungateiclostridium thermocellum was modeled by homology modeling. The catalytic module (HtGH9t) of HtGH9 modeled structure displayed the (?/?)6 barrel topology and associated family 3 carbohydrate binding module (HtCBM3c) displayed ?-sandwich fold. Ramachandran plot of HtGH9 modeled structure displayed all the amino acid residues in allowed region except Asn225 and Asp317. Secondary structure analysis of modeled HtGH9 showed the presence of 41.3% ?-helices and 11.0% ?-strands which was validated through circular dichroism analysis that showed the presence of 42.6% ?-helices and 14.5% ?-strands. Molecular Dynamic (MD) simulation of HtGH9 structure for 50 ns showed Root Mean Square Deviation (RMSD), 0.84 nm and radius of gyration (Rg) 3.1 nm. The Small-angle X-ray scattering of HtGH9 confirmed the monodisperse state. The radius of gyration for globular shape (Rg) was 5.50�0.15 nm and for rod shape (Rc) by Guinier plot was 2.0 nm. The loop formed by amino acid residues, 264-276 towards one end of the catalytic site of HtGH9 forms a barrier, that blocks the non-reducing end of the cellulose chain causing the processive cleavage resulting in the release of cellotetraose. The position of the corresponding loop in cellulases of family 9 GH is responsible for different types of cleavage patterns.
dc.description.statementofresponsibility by Krishan Kumar, Shubha Singh, Kedar Sharma and Arun Goyal
dc.language.iso en_US en_US
dc.publisher Elsevier en_US
dc.subject Hungateiclostridium Thermocellum en_US
dc.subject Family 9 Glycoside Hydrolase en_US
dc.subject Processive Endocellulase en_US
dc.subject Molecular Dynamic Simulation en_US
dc.subject Small-angle X-ray Scattering en_US
dc.title 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 en_US
dc.type Article en_US
dc.relation.journal Journal of Molecular Graphics and Modelling


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