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Molecular dynamics–based structural insights of the first putative endoglucanase, PsGH5A of glycoside hydrolase family 5 from Pseudopedobacter saltans

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Abstract

Context

The putative endoglucanase, PsGH5A, from Pseudopedobacter saltans of family GH5 contains a catalytic module, PsGH5 (β/α)8-TIM barrel), at N-terminal followed by a family 6 carbohydrate-binding module (CBM6, β-sandwich). Superposition of PsGH5A with PDB homologs revealed Glu220 and Glu318 as evolutionarily conserved and catalytic residues performing the hydrolysis through retaining-type mechanism, a canonical property of GH5 family. PsGH5A showed higher affinity for longer cellooligosaccharides, as long as cellodecaose with binding free energy (∆G) of − 13.72 kcal/mol upon the molecular docking, thereby indicating the endo-mode of hydrolysis. The radius of gyration, Rg (2.7 nm), and solvent accessible surface area, SASA (229.6 nm2), of PsGH5A-Cellotetraose complex were determined by MD simulation which was lower than that of PsGH5A (Rg, 2.8 nm, SASA, 267 nm2) demonstrating the compactness and affinity of PsGH5A with the cellulosic ligands. Cellulose compatibility of PsGH5A was further confirmed by MMPBSA and per-residue decomposition analysis, where notable ∆G of − 54.38 kcal/mol for PsGH5A-Cellotetraose complex was observed. Thus, PsGH5A could be potentially an efficient endoglucanase as it accommodated larger cellooligosaccharides at its active-site. PsGH5A is the first putative endoglucanase studied here from P. saltans which could be genome-mined for lignocellulosic biomass saccharification in the renewable energy sector.

Methods

The 3-D structure of PsGH5A generated by AlphaFold2, RaptorX, SwissModel, Phyre2 and Robetta tool; YASARA was used for energy minimization of built models. UCLA SAVES-v6 was used for quality assessment of models. Molecular Docking was performed using SWISS-DOCK server and Chimera software. Molecular Dynamics simulations and MMPBSA analysis of PsGH5A and PsGH5A-Cellotetraose complex were performed on GROMACS 2019.6.

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Data availability

The datasets generated during and analysed during the current study are available from the corresponding author on reasonable request.

Abbreviations

EC:

Enzyme commission

CBH:

Cellobiohydrolase

PSI-BLAST:

Position-Specific Iterative Basic Local Alignment Search Tool

TIM:

Triose phosphate isomerase

AA:

Amino acids

NCBI:

National Center for Biotechnology Information

EMBL:

European Molecular Biology Laboratory

PDB:

Protein Data Bank

UCLA:

University of California

HTC:

High-throughput computing

NVT:

Normal Volume Temperature

NPT:

Normal Pressure Temperature

RMSD:

Root Mean Square Deviation

RMSF:

Root Mean Square Fluctuation

SD:

Standard Dviation

MMPBSA:

Molecular Mechanics Poisson-Boltzmann Surface Area

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Acknowledgements

PVG is thankful to the Ministry of Education (erstwhile, Ministry of Human Resource Development (MHRD), Govt. of India, for the fellowship through Graduate Aptitude Test for Engineering (GATE). The authors also thank Param-Ishan Supercomputing facility at IIT Guwahati for molecular simulations.

Funding

The research work was supported by a Trilateral project with the Indian Institute of Technology Bombay, Mumbai, India and All India Institute of Medical Sciences (AIIMS), New Delhi, India under the NERBPMC DBT-Twinning project scheme with the grant (No. BT/PR24786/NER/95/853/2017) from Department of Biotechnology, Ministry of Science and Technology, New Delhi, Government of India to AG.

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Authors and Affiliations

  1. Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India

    Parmeshwar Vitthal Gavande & Arun Goyal

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  1. Parmeshwar Vitthal Gavande
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Contributions

Parmeshwar Vitthal Gavande: methodology, investigation, visualization, software and data curation, formal analysis, validation, writing—original draft preparation, rewriting and editing. Arun Goyal: conceptualization, supervision, resources, project administration, reviewing, rewriting, editing.

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Correspondence to Arun Goyal.

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This research did not involve any human participants or animals to generate and analyse the data used in this study.

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Highlights

• PsGH5A contains canonical (β/α)8-TIM barrel for catalytic module.

• Associated CBM6 module possesses β-sandwich fold.

• PsGH5A with Glu220 and Glu318 catalytic residues shows retaining-type mechanism.

• MD simulation of PsGH5A-Cellotetraose complex showed stability and compactness.

• PsGH5A active-site can accommodate cellulosic ligands as large as cellodecaose.

• ∆G by MMPBSA indicated higher affinity of PsGH5A for cellulosic ligands.

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Gavande, P.V., Goyal, A. Molecular dynamics–based structural insights of the first putative endoglucanase, PsGH5A of glycoside hydrolase family 5 from Pseudopedobacter saltans. J Mol Model 29, 186 (2023). https://doi.org/10.1007/s00894-023-05575-8

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