Characterization of dye-decolorizing peroxidase from Bacillus subtilis

Dhankhar, Poonam; Dalal, Vikram; Mahto, Jai Krishna; Gurjar, Bhola R.; Tomar, Shailly; Sharma, Ashwani; Kumar, Pravindra

doi:10.1016/j.abb.2020.108590

Cited by 68 publications

(54 citation statements)

References 89 publications

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“…of 0.31 Å between Cα atoms. The recently deposited Bs DyP crystal structure (PDB 6KMN, [ 35 ]) belongs to the triclinic P1 space group, showing four subunits in the asymmetric unit. The crystal structure of the 5G5 variant belongs to the monoclinic P21 space group and four monomers in the asymmetric unit were identified.…”

Section: Resultsmentioning

confidence: 99%

“…The side chains of D240 and R339 are oriented to the heme iron, with a D240 OD1 –Fe distance of 5.2–5.5 Å and R339 NH2 –Fe distance of 4.1–4.6 Å, similar to those measured in the reported Bs DyP structure (PDB 6KMN). A water molecule is located approximately at 3.5 Å apart from the iron atom ( Figure S6b ); in the heme pocket of the 6KMN structure, an electron density blob was fitted with molecular oxygen, where the closest oxygen atom to the iron atom is at a 3.4 Å distance [ 35 ]. Access to the heme from the surface, as defined using a 1.4-Å rolling probe, is made through a distal tunnel and an open wide cavity ( Figure 3 a and Figure S6c,d and Tables S4–S6 ).…”

Section: Resultsmentioning

confidence: 99%

“…The open wide cavity gives access to the solvent-exposed heme propionate p6 group and likely represents an electron transfer route from substrates to the porphyrin radical [ 40 , 41 ]. Bs DyP structure PDB 6KMM unveiled the presence of two HEPES molecules: one is bound at 6 Å away from the propionate group in the heme cavity and another at 16 Å near the surface-exposed Y388 residue ( Figure S7a,b ) [ 35 ]. Moreover, the docking of HEPES and three different synthetic dyes using snapshots from molecular dynamics simulations of Bs DyP also indicated two putative binding sites for reduced substrates [ 35 ].…”

Section: Resultsmentioning

confidence: 99%

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Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis

Rodrigues

Borges

Scocozza

et al. 2021

IJMS

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Bacillus subtilis BsDyP belongs to class I of the dye-decolorizing peroxidase (DyP) family of enzymes and is an interesting biocatalyst due to its high redox potential, broad substrate spectrum and thermostability. This work reports the optimization of BsDyP using directed evolution for improved oxidation of 2,6-dimethoxyphenol, a model lignin-derived phenolic. After three rounds of evolution, one variant was identified displaying 7-fold higher catalytic rates and higher production yields as compared to the wild-type enzyme. The analysis of X-ray structures of the wild type and the evolved variant showed that the heme pocket is delimited by three long conserved loop regions and a small α helix where, incidentally, the mutations were inserted in the course of evolution. One loop in the proximal side of the heme pocket becomes more flexible in the evolved variant and the size of the active site cavity is increased, as well as the width of its mouth, resulting in an enhanced exposure of the heme to solvent. These conformational changes have a positive functional role in facilitating electron transfer from the substrate to the enzyme. However, they concomitantly resulted in decreasing the enzyme’s overall stability by 2 kcal mol−1, indicating a trade-off between functionality and stability. Furthermore, the evolved variant exhibited slightly reduced thermal stability compared to the wild type. The obtained data indicate that understanding the role of loops close to the heme pocket in the catalysis and stability of DyPs is critical for the development of new and more powerful biocatalysts: loops can be modulated for tuning important DyP properties such as activity, specificity and stability.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis

Rodrigues

Borges

Scocozza

et al. 2021

IJMS

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“…The final hits from pharmacophore screening were utilized for virtual screening using the crystal structure of NTD-N-protein. Virtual screening, molecular docking and dynamics have been widely used techniques to identify the potent lead molecules and assess the stability of protein-ligand complexes (Dalal et al, 2019;Dhankhar, Dalal, Mahto, et al, 2020;Gau et al, 2018;Meng et al, 2015). Out of the top 50 molecules, three molecules (ZINC000257324845, ZINC000005169973 and ZINC000009913056) were successfully passed the ADMET filters and also having druglike properties, which were analysed by Lipinski's rule of five.…”

Section: Discussionmentioning

confidence: 99%

Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2

Dhankhar

Dalal

Singh

et al. 2020

Journal of Biomolecular Structure and Dynamics

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The Coronavirus Disease 2019, caused by the severe acute respiratory syndrome coronavirus 2 is an exceptionally contagious disease that leads to global epidemics with elevated mortality and morbidity. There are currently no efficacious drugs targeting coronavirus disease 2019, therefore, it is an urgent requirement for the development of drugs to control this emerging disease. Owing to the importance of nucleocapsid protein, the present study focuses on targeting the N-terminal domain of nucleocapsid protein from severe acute respiratory syndrome coronavirus 2 to identify the potential compounds by computational approaches such as pharmacophore modeling, virtual screening, docking and molecular dynamics. We found three molecules (ZINC000257324845, ZINC000005169973 and ZINC000009913056), which adopted a similar conformation as guanosine monophosphate (GMP) within the N-terminal domain active site and exhibiting high binding affinity (>À8.0 kcalmol À1). All the identified compounds were stabilized by hydrogen bonding with Arg107, Tyr111 and Arg149 of Nterminal domain. Additionally, the aromatic ring of lead molecules formed p interactions with Tyr109 of N-terminal domain. Molecular dynamics and Molecular mechanic/Poisson-Boltzmann surface area results revealed that N-terminal domainligand(s) complexes are less dynamic and more stable than N-terminal domain-GMP complex. As the identified compounds share the same corresponding pharmacophore properties, therefore, the present results may serve as a potential lead for the development of inhibitors against severe acute respiratory syndrome coronavirus 2.

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“…Note that both oxidation and N-demethylation reactions were reported for MG catalyzed by natural enzymes, such as laccase and heme enzymes. 10,13,37,38 Therefore, the articial enzyme of F43H/H64A Mb exhibited a general mechanism for the biodegradation of MG, which makes it an ideal alternative to that of natural enzymes.…”

Section: Product Analysis Of Mg Degradation By F43h/h64a Mbmentioning

confidence: 99%

Efficient biodegradation of malachite green by an artificial enzyme designed in myoglobin

Xiang

Liu

et al. 2021

RSC Adv.

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Characterization of dye-decolorizing peroxidase from Bacillus subtilis

Cited by 68 publications

References 89 publications

Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis

Loops around the Heme Pocket Have a Critical Role in the Function and Stability of BsDyP from Bacillus subtilis

Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2

Efficient biodegradation of malachite green by an artificial enzyme designed in myoglobin

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