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Article ; Online: Crystal structure of a thiolase from Archaeal Pyrococcus furiosus and its in silico functional annotation.

Singh, Rashika / Mishra, Vipin Kumar / Das, Amit Kumar

Biochemical and biophysical research communications

2023 Volume 693, Page(s) 149377

Abstract: In most of the eukaryotes and archaea, isopentenyl pyrophosphate (IPP) and dimethyl allyl pyrophosphate (DMAPP) essential building blocks of all isoprenoids synthesized in the mevalonate pathway. Here, the first enzyme of this pathway, acetoacetyl CoA ... ...

Abstract	In most of the eukaryotes and archaea, isopentenyl pyrophosphate (IPP) and dimethyl allyl pyrophosphate (DMAPP) essential building blocks of all isoprenoids synthesized in the mevalonate pathway. Here, the first enzyme of this pathway, acetoacetyl CoA thiolase (PFC_04095) from an archaea Pyrococcus furiosus is structurally characterized. The crystal structure of PFC_04095 is determined at 2.7 Å resolution, and the crystal structure reveals the absence of catalytic acid/base cysteine in its active site, which is uncommon in thiolases. In place of cysteine, His285 of HDAF motif performs both protonation and abstraction of proton during the reaction. The crystal structure shows that the distance between Cys83 and His335 is 5.4 Å. So, His335 could not abstract a proton from nucleophilic cysteine (Cys83), resulting in the loss of enzymatic activity of PFC_04095. MD simulations of the docked PFC_04095-acetyl CoA complex show substrate binding instability to the active site pocket. Here, we have reported that the stable binding of acetyl CoA to the PFC_04095 pocket requires the involvement of three protein complexes, i.e., thiolase (PFC_04095), DUF35 (PFC_04100), and HMGCS (PFC_04090).
MeSH term(s)	Acetyl-CoA C-Acetyltransferase/chemistry ; Acetyl Coenzyme A/metabolism ; Pyrococcus furiosus/metabolism ; Cysteine/metabolism ; Protons ; Models, Molecular
Chemical Substances	Acetyl-CoA C-Acetyltransferase (EC 2.3.1.9) ; Acetyl Coenzyme A (72-89-9) ; Cysteine (K848JZ4886) ; Protons
Language	English
Publishing date	2023-12-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2023.149377
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Article ; Online: Identification, trace level quantification, and

Sayyed, Faiz Hussain / Rathod, Nitin / Mishra, Vipin Kumar / Nalawade, Vighnesh / Roy, Bappaditya

Drug and chemical toxicology

2024 , Page(s) 1–9

Abstract: Potential genotoxic impurities in medications are an increasing concern in the pharmaceutical industry and regulatory bodies because of the risk of human carcinogenesis. To prevent the emergence of these impurities, it is crucial to carefully examine not ...

Abstract	Potential genotoxic impurities in medications are an increasing concern in the pharmaceutical industry and regulatory bodies because of the risk of human carcinogenesis. To prevent the emergence of these impurities, it is crucial to carefully examine not only the final product but also the intermediates and key starting material (KSM) used in drug synthesis. During the related substances analysis of KSM of Famotidine, an unknown impurity in the range of 0.5-1.0% was found prompting the need for isolation and characterization due to the possibility of its to infiltrate into the final product. In this study, the impurity was isolated and characterized as 5-(2-chloroethyl)-3,3-dimethyl-3,4-dihydro-2H-1,2,4,6-thiatriazine 1,1-dioxide using multiple instrumental analysis, uncovering a structural alert that raises concern. Considering the potential impact of impurity on human health, an
Language	English
Publishing date	2024-03-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	548368-2
ISSN	1525-6014 ; 0148-0545
ISSN (online)	1525-6014
ISSN	0148-0545
DOI	10.1080/01480545.2024.2321941
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Article ; Online: Design, Synthesis, and Characterization of Organometallic BODIPY-Ru(II) Dyads: Redox and Photophysical Properties with Singlet Oxygen Generation Capability†.

Maity, Apurba / Mishra, Vipin Kumar / Dolai, Suman / Mishra, Sabyashachi / Patra, Sanjib K

Inorganic chemistry

2024 Volume 63, Issue 11, Page(s) 4839–4854

Abstract: A series of Ru(II)-acetylide complexes ( ...

Abstract	A series of Ru(II)-acetylide complexes (
Language	English
Publishing date	2024-03-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	1484438-2
ISSN	1520-510X ; 0020-1669
ISSN (online)	1520-510X
ISSN	0020-1669
DOI	10.1021/acs.inorgchem.3c03610
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Article ; Online: Flipped regiospecificity in L434F mutant of 8-lipoxygenase.

Mishra, Vipin Kumar / Mishra, Sabyashachi

Physical chemistry chemical physics : PCCP

2020 Volume 22, Issue 28, Page(s) 16013–16022

Abstract: Lipoxygenases are non-heme iron containing enzymes that catalyze oxygenation of poly-unsaturated fatty acids in different animal and plant species with extremely high regio- and stereospecificity. Nature employs 8-lipoxygenase to produce 8R-hydroperoxide ...

Abstract	Lipoxygenases are non-heme iron containing enzymes that catalyze oxygenation of poly-unsaturated fatty acids in different animal and plant species with extremely high regio- and stereospecificity. Nature employs 8-lipoxygenase to produce 8R-hydroperoxide from the oxygenation of arachidonic acid. A single-point L434F mutation of 8-lipoxygenase alters the regio- and stereospecificity of the final products, with a product ratio of 66 : 34 for 8R- and 12S-hydroperoxide, respectively. A molecular level explanation of this flipped regiospecificity is presented in this work on the basis of molecular dynamics simulations and transition network analysis of oxygen migration in the protein matrix. Phe434 is shown to exist in two conformations, the so-called open and closed conformations. In the closed conformation, the phenyl group of Phe434 shields the C8 site of the substrate, thereby preventing access of the oxygen molecule to this site, which leads to a quenching of the 8R-product. On the other hand, both closed and open conformations of Phe434 allow the oxygen molecule to approach the pro-S face of the C12 site of the substrate, which enhances the propensity of the 12S-hydroperoxide.
MeSH term(s)	Animals ; Arachidonate Lipoxygenases/chemistry ; Arachidonate Lipoxygenases/genetics ; Arachidonate Lipoxygenases/metabolism ; Crystallography, X-Ray ; Molecular Dynamics Simulation ; Mutation ; Protein Conformation
Chemical Substances	Arachidonate Lipoxygenases (EC 1.13.11.-) ; arachidonate 8-lipoxygenase (EC 1.13.11.40)
Language	English
Publishing date	2020-07-06
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d0cp02351e
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Article ; Online: Origin of Regio- and Stereospecific Catalysis by 8-Lipoxygenase.

Mishra, Vipin Kumar / Mishra, Sabyashachi

The journal of physical chemistry. B

2019 Volume 123, Issue 50, Page(s) 10605–10621

Abstract: Lipoxygenases (lox's) are a group of non-heme iron containing enzymes that catalyze oxygenation of polyunsaturated fatty acids with precise regio- and stereoselectivities. The origin of regio- and stereospecific catalysis by 8-lox is explored in its wild- ...

Abstract	Lipoxygenases (lox's) are a group of non-heme iron containing enzymes that catalyze oxygenation of polyunsaturated fatty acids with precise regio- and stereoselectivities. The origin of regio- and stereospecific catalysis by 8-lox is explored in its wild-type (wt) form and in three mutants (Arg185Ala, Ala592Met, and Ala623His). The catalytic action of this enzyme progresses in two steps, namely, hydrogen abstraction from one double allylic carbon atom of substrate followed by oxygen insertion at the resulting prochiral carbon radical of the substrate. It is shown that the positional specificity of the hydrogen abstraction is a result of conformational dynamics of the bound substrate. While the C10 atom of the substrate is found to be the most probable site of hydrogen abstraction in the wt-lox, hydrogen abstraction from C13 is more favorable in the mutants. The present study discovers the presence of an interconnected network of a three-channel migration pathway operating in the protein matrix for efficient oxygen transport. Each migration channel is bestowed with a pocket at the peripheral region of protein as an oxygen access site, which transfers the oxygen to the active site through a well-connected migration path on a time scale of a few hundred picoseconds. By a careful geometric analysis of the oxygen pockets near the substrate binding cleft, the present study identifies the launching sites for oxygenation at the prochiral carbon centers C8, C11, C12, and C15 and the stereochemistry (
MeSH term(s)	Arachidonate Lipoxygenases/chemistry ; Arachidonate Lipoxygenases/genetics ; Arachidonate Lipoxygenases/metabolism ; Biocatalysis ; Molecular Dynamics Simulation ; Mutation ; Protein Conformation ; Stereoisomerism ; Substrate Specificity
Chemical Substances	Arachidonate Lipoxygenases (EC 1.13.11.-) ; arachidonate 8-lipoxygenase (EC 1.13.11.40)
Language	English
Publishing date	2019-12-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.9b07917
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Article ; Online: Crystal structure of FadA2 thiolase from Mycobacterium tuberculosis and prediction of its substrate specificity and membrane-anchoring properties.

Singh, Rashika / Kundu, Prasun / Mishra, Vipin Kumar / Singh, Bina Kumari / Bhattacharyya, Sudipta / Das, Amit Kumar

The FEBS journal

2023 Volume 290, Issue 16, Page(s) 3997–4022

Abstract: Tuberculosis (TB) is one of the leading causes of human death caused by Mycobacterium tuberculosis (Mtb). Mtb can enter into a long-lasting persistence where it can utilize fatty acids as the carbon source. Hence, fatty acid metabolism pathway enzymes ... ...

Abstract	Tuberculosis (TB) is one of the leading causes of human death caused by Mycobacterium tuberculosis (Mtb). Mtb can enter into a long-lasting persistence where it can utilize fatty acids as the carbon source. Hence, fatty acid metabolism pathway enzymes are considered promising and pertinent mycobacterial drug targets. FadA2 (thiolase) is one of the enzymes involved in Mtb's fatty acid metabolism pathway. FadA2 deletion construct (ΔL136-S150) was designed to produce soluble protein. The crystal structure of FadA2 (ΔL136-S150) at 2.9 Å resolution was solved and analysed for membrane-anchoring region. The four catalytic residues of FadA2 are Cys99, His341, His390 and Cys427, and they belong to four loops with characteristic sequence motifs, i.e., CxT, HEAF, GHP and CxA. FadA2 is the only thiolase of Mtb which belongs to the CHH category containing the HEAF motif. Analysing the substrate-binding channel, it has been suggested that FadA2 is involved in the β-oxidation pathway, i.e., the degradative pathway, as the long-chain fatty acid can be accommodated in the channel. The catalysed reaction is favoured by the presence of two oxyanion holes, i.e., OAH1 and OAH2. OAH1 formation is unique in FadA2, formed by the NE2 of His390 present in the GHP motif and NE2 of His341 present in the HEAF motif, whereas OAH2 formation is similar to CNH category thiolase. Sequence and structural comparison with the human trifunctional enzyme (HsTFE-β) suggests the membrane-anchoring region in FadA2. Molecular dynamics simulations of FadA2 with a membrane containing POPE lipid were conducted to understand the role of a long insertion sequence of FadA2 in membrane anchoring.
MeSH term(s)	Humans ; Mycobacterium tuberculosis/metabolism ; Substrate Specificity ; Acetyl-CoA C-Acetyltransferase/chemistry ; Acetyl-CoA C-Acetyltransferase/metabolism
Chemical Substances	Acetyl-CoA C-Acetyltransferase (EC 2.3.1.9)
Language	English
Publishing date	2023-04-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16792
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Article: Origin of Regio- and Stereospecific Catalysis by 8-Lipoxygenase

Mishra, Vipin Kumar / Mishra, Sabyashachi

Journal of physical chemistry. 2019 Nov. 27, v. 123, no. 50

2019

Abstract: Lipoxygenases (lox’s) are a group of non-heme iron containing enzymes that catalyze oxygenation of polyunsaturated fatty acids with precise regio- and stereoselectivities. The origin of regio- and stereospecific catalysis by 8-lox is explored in its wild- ...

Abstract	Lipoxygenases (lox’s) are a group of non-heme iron containing enzymes that catalyze oxygenation of polyunsaturated fatty acids with precise regio- and stereoselectivities. The origin of regio- and stereospecific catalysis by 8-lox is explored in its wild-type (wt) form and in three mutants (Arg185Ala, Ala592Met, and Ala623His). The catalytic action of this enzyme progresses in two steps, namely, hydrogen abstraction from one double allylic carbon atom of substrate followed by oxygen insertion at the resulting prochiral carbon radical of the substrate. It is shown that the positional specificity of the hydrogen abstraction is a result of conformational dynamics of the bound substrate. While the C10 atom of the substrate is found to be the most probable site of hydrogen abstraction in the wt-lox, hydrogen abstraction from C13 is more favorable in the mutants. The present study discovers the presence of an interconnected network of a three-channel migration pathway operating in the protein matrix for efficient oxygen transport. Each migration channel is bestowed with a pocket at the peripheral region of protein as an oxygen access site, which transfers the oxygen to the active site through a well-connected migration path on a time scale of a few hundred picoseconds. By a careful geometric analysis of the oxygen pockets near the substrate binding cleft, the present study identifies the launching sites for oxygenation at the prochiral carbon centers C8, C11, C12, and C15 and the stereochemistry (R/S) of the corresponding products. It is found that the dominating 8R product in the wt-lox is due to the presence of the aromatic ring pair of Tyr181 and Phe173 acting as a gatekeeper for efficient delivery of oxygen at the pro-R face of C8. The change in the stereochemistry of the products in mutants is explained in terms of dynamic interactions between substrate and the surrounding residues.
Keywords	active sites ; aromatic compounds ; carbon ; catalytic activity ; geometry ; hydrogen ; iron ; lipoxygenases ; mutants ; oxygen ; polyunsaturated fatty acids ; stereochemistry ; stereospecificity
Language	English
Dates of publication	2019-1127
Size	p. 10605-10621.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021/acs.jpcb.9b07917
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Article ; Online: Crystal structure of FadA2 thiolase from Mycobacterium tuberculosis and prediction of its substrate specificity and membrane‐anchoring properties

Singh, Rashika / Kundu, Prasun / Mishra, Vipin Kumar / Singh, Bina Kumari / Bhattacharyya, Sudipta / Das, Amit Kumar

The FEBS Journal. 2023 Aug., v. 290, no. 16 p.3997-4022

2023

Abstract: Tuberculosis (TB) is one of the leading causes of human death caused by Mycobacterium tuberculosis (Mtb). Mtb can enter into a long‐lasting persistence where it can utilize fatty acids as the carbon source. Hence, fatty acid metabolism pathway enzymes ... ...

Abstract	Tuberculosis (TB) is one of the leading causes of human death caused by Mycobacterium tuberculosis (Mtb). Mtb can enter into a long‐lasting persistence where it can utilize fatty acids as the carbon source. Hence, fatty acid metabolism pathway enzymes are considered promising and pertinent mycobacterial drug targets. FadA2 (thiolase) is one of the enzymes involved in Mtb's fatty acid metabolism pathway. FadA2 deletion construct (ΔL136‐S150) was designed to produce soluble protein. The crystal structure of FadA2 (ΔL136‐S150) at 2.9 Å resolution was solved and analysed for membrane‐anchoring region. The four catalytic residues of FadA2 are Cys99, His341, His390 and Cys427, and they belong to four loops with characteristic sequence motifs, i.e., CxT, HEAF, GHP and CxA. FadA2 is the only thiolase of Mtb which belongs to the CHH category containing the HEAF motif. Analysing the substrate‐binding channel, it has been suggested that FadA2 is involved in the β‐oxidation pathway, i.e., the degradative pathway, as the long‐chain fatty acid can be accommodated in the channel. The catalysed reaction is favoured by the presence of two oxyanion holes, i.e., OAH1 and OAH2. OAH1 formation is unique in FadA2, formed by the NE2 of His390 present in the GHP motif and NE2 of His341 present in the HEAF motif, whereas OAH2 formation is similar to CNH category thiolase. Sequence and structural comparison with the human trifunctional enzyme (HsTFE‐β) suggests the membrane‐anchoring region in FadA2. Molecular dynamics simulations of FadA2 with a membrane containing POPE lipid were conducted to understand the role of a long insertion sequence of FadA2 in membrane anchoring.
Keywords	Mycobacterium tuberculosis ; carbon ; catalytic activity ; crystal structure ; death ; drugs ; enzymes ; fatty acid metabolism ; humans ; long chain fatty acids ; molecular dynamics ; oxyanions ; prediction ; substrate specificity ; transposons ; tuberculosis
Language	English
Dates of publication	2023-08
Size	p. 3997-4022.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16792
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Translesion Synthesis across the

Boldinova, Elizaveta O / Ghodke, Pratibha P / Sudhakar, Sruthi / Mishra, Vipin Kumar / Manukyan, Anna A / Miropolskaya, Nataliya / Pradeepkumar, Pushpangadan I / Makarova, Alena V

ACS chemical biology

2022 Volume 17, Issue 11, Page(s) 3238–3250

Abstract: Primase-DNA polymerase (PrimPol) is involved in reinitiating DNA synthesis at stalled replication forks. PrimPol also possesses DNA translesion (TLS) activity and bypasses several endogenous nonbulky DNA lesions in vitro. Little is known about the TLS ... ...

Abstract	Primase-DNA polymerase (PrimPol) is involved in reinitiating DNA synthesis at stalled replication forks. PrimPol also possesses DNA translesion (TLS) activity and bypasses several endogenous nonbulky DNA lesions in vitro. Little is known about the TLS activity of PrimPol across bulky carcinogenic adducts. We analyzed the DNA polymerase activity of human PrimPol on DNA templates with seven
MeSH term(s)	Humans ; Deoxycytidine Monophosphate ; DNA Damage ; Deoxyguanosine/chemistry ; DNA Replication ; DNA-Directed DNA Polymerase/metabolism ; DNA/chemistry ; DNA Adducts ; Nuclear Proteins/metabolism ; DNA Primase/metabolism ; Multifunctional Enzymes/metabolism
Chemical Substances	Deoxycytidine Monophosphate (1032-65-1) ; Deoxyguanosine (G9481N71RO) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; DNA (9007-49-2) ; DNA Adducts ; POLDIP2 protein, human ; Nuclear Proteins ; PrimPol protein, human (EC 2.7.7.-) ; DNA Primase (EC 2.7.7.-) ; Multifunctional Enzymes
Language	English
Publishing date	2022-11-01
Publishing country	United States
Document type	Journal Article
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.2c00717
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Article: Through bond energy transfer (TBET)-operated fluoride ion sensing via spirolactam ring opening of a coumarin–fluorescein bichromophoric dyad

Padhan, Subrata Kumar / Mishra, Vipin Kumar / Murmu, Narayan / Mishra, Sabyashachi / Sahu, Satya Narayan

RSC advances. 2020 July 30, v. 10, no. 47

2020

Abstract: The detection of fluoride ions in a competitive environment often poses several challenges. In this work, we have designed and synthesized a coumarin functionalized fluorescein dyad (R3) which represents an ideal through bond energy transfer (TBET) ... ...

Abstract	The detection of fluoride ions in a competitive environment often poses several challenges. In this work, we have designed and synthesized a coumarin functionalized fluorescein dyad (R3) which represents an ideal through bond energy transfer (TBET) fluorophore with the coumarin unit as donor and fluorescein unit as acceptor. The bichromophoric dyad demonstrates the detection of fluoride ions in the parts per billion (ppb) concentration level (22.8 ppb) with high selectivity via a TBET emission signal at 548 nm with a diagnostic bright yellow colour fluorescence output. Based on UV-visible, fluorescence, ¹H NMR and DFT studies, it is shown that the fluoride ion induces the opening of the spirolactam ring of the fluorescein moiety and provides a π-conjugation link between the donor and acceptor units enabling a TBET phenomenon with a larger pseudo-Stokes shift of 172 nm. To the best of our knowledge, this is the first report where the fluoride ion is detected via a TBET signal between the coumarin and fluorescein units in a bichromophoric dyad.
Keywords	color ; coumarin ; energy transfer ; fluorescein ; fluorescence ; fluorides ; moieties
Language	English
Dates of publication	2020-0730
Size	p. 28422-28430.
Publishing place	The Royal Society of Chemistry
Document type	Article
Note	NAL-AP-2-clean
ISSN	2046-2069
DOI	10.1039/d0ra05357k
Database	NAL-Catalogue (AGRICOLA)

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