Free energy landscapes of prototropic tautomerism in pyridoxal 5′‐phosphate schiff bases at the active site of an enzyme in aqueous medium

Soniya, Kumari; Chandra, Amalendu

doi:10.1002/jcc.25338

Cited by 13 publications

(27 citation statements)

References 53 publications

(58 reference statements)

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“…The hydroxyl group of the serine substrate is found to be hydrogen bonded to the active site Glu′53 residue and the phenolic oxygen (O3A) is found to lie close to the active site Ser172 residue. Also, the external aldimine that is produced at the end of the transimination reaction is found to be in the ketoenamine form with proton staying with the imine nitrogen, which is consistent with the earlier results of the keto-enol tautomerism of the SER-PLP external aldimine at the active site of SHMT …”

Section: Discussionsupporting

confidence: 91%

“…The phosphate group of PLP is deeply buried inside the protein and acts as an anchor to keep the coenzyme at the right position during catalysis. Also, the PLP-LYS internal aldimine was found to favor the ketoenamine tautomer over the enolimine tautomer at the active site of SHMT . In this paper, the transimination reaction is studied for SHMT starting from the ketoenamine form of the PLP-LYS internal aldimine by employing hybrid quantum mechanical/molecular mechanical (QM/MM) simulations , combined with the metadynamics method of rare event sampling. − Specifically, we have studied the free energy landscape and mechanism of the transimination reaction for conversion of PLP-LYS (SHMT) internal aldimine to the PLP-serine (substrate) external aldimine at the active site of the SHMT enzyme in aqueous medium.…”

Section: Introductionmentioning

confidence: 99%

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Free Energy Landscape and Proton Transfer Pathways of the Transimination Reaction at the Active site of the Serine Hydroxymethyltransferase Enzyme in Aqueous Medium

Soniya

Chandra

2021

J. Phys. Chem. B

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Serine hydroxymethyltransferase (SHMT) is a ubiquitous enzyme belonging to the fold type I or aspartate aminotransferase (AspAT) family of the pyridoxal 5′-phosphate (PLP)dependent enzymes. Like other PLP-dependent enzymes, SHMT also undergoes the so-called transimination reaction before exhibiting its enzymatic activity. The transimination process constitutes an important pre-step for all PLP-dependent enzymes, where an internal aldimine of the PLP−enzyme complex gets converted to an external aldimine of the substrate−PLP complex at the active site of the enzyme. In case of the transimination reaction involving SHMT, the PLP molecule bound to the active site lysine residue of SHMT (internal aldimine) gets detached from the enzyme by a serine substrate to produce an external aldimine complex, where the PLP is now bound to the serine substrate. In the current study, the free energy surfaces and reaction pathways of different steps of the transimination reaction at the active site of SHMT are investigated by employing hybrid quantum mechanical/molecular mechanical (QM/MM) simulations combined with metadynamics methods of rare event sampling. It is found that the process of transimination involving serine and PLP at the active site of the SHMT enzyme takes place through different elementary steps such as the formation of the first geminal diamine intermediate (GDI1), transfer of a proton from the substrate serine to the phenolic oxygen of PLP, followed by another proton transfer from PLP to the amine nitrogen of lysine with the formation of the second geminal diamine intermediate (GDI2), and finally, detachment of the active site lysine residue from PLP to produce the external aldimine.

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Section: Discussionsupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Free Energy Landscape and Proton Transfer Pathways of the Transimination Reaction at the Active site of the Serine Hydroxymethyltransferase Enzyme in Aqueous Medium

Soniya

Chandra

2021

J. Phys. Chem. B

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“…The initial 345-nm peak formed upon L-cysteine binding to H123A SufS is assigned as the enolimine tau-tomer of the Cys-aldimine that is slightly red-shifted by loss of the nearby histidine and itsstacking interaction. This assignment is also consistent with known PLP chemistry because the enolimine is predicted to be the more reactive of the Cys-aldimine tautomers and would logically proceed to the Cys-ketimine seen at 350 nm (35,36).…”

Section: Role Of His-123 and Cys-364 In The Sufs Mechanismsupporting

confidence: 81%

“…3-5). A similar phenomenon is predicted by metadynamics calculations carried out on the PLP-dependent serine hydroxymethyltransferase (SHMT) enzyme (35). Those previous studies suggested that theinteraction of the PLP pyridine ring with SHMT His-122 is weakened in the enolimine tautomer of the external aldimine of SHMT.…”

Section: A Role For His-123 As An Acid-base Catalystsupporting

confidence: 72%

Direct observation of intermediates in the SufS cysteine desulfurase reaction reveals functional roles of conserved active-site residues

Blahut

Wise

Bruno

et al. 2019

Journal of Biological Chemistry

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Iron-sulfur (Fe-S) clusters are necessary for the proper functioning of numerous metalloproteins. Fe-S cluster (Isc) and sulfur utilization factor (Suf) pathways are the key biosynthetic routes responsible for generating these Fe-S cluster prosthetic groups in Escherichia coli. Although Isc dominates under normal conditions, Suf takes over during periods of iron depletion and oxidative stress. Sulfur acquisition via these systems relies on the ability to remove sulfur from free cysteine using a cysteine desulfurase mechanism. In the Suf pathway, the dimeric SufS protein uses the cofactor pyridoxal 5-phosphate (PLP) to abstract sulfur from free cysteine, resulting in the production of alanine and persulfide. Despite much progress, the stepwise mechanism by which this PLP-dependent enzyme operates remains unclear. Here, using rapid-mixing kinetics in conjunction with X-ray crystallography, we analyzed the pre-steadystate kinetics of this process while assigning early intermediates of the mechanism. We employed H123A and C364A SufS variants to trap Cys-aldimine and Cys-ketimine intermediates of the cysteine desulfurase reaction, enabling direct observations of these intermediates and associated conformational changes of the SufS active site. Of note, we propose that Cys-364 is essential for positioning the Cys-aldimine for C␣ deprotonation, His-123 acts to protonate the Ala-enamine intermediate, and Arg-56 facilitates catalysis by hydrogen bonding with the sulfhydryl of Cys-aldimine. Our results, along with previous SufS structural findings, suggest a detailed model of the SufS-catalyzed reaction from Cys binding to C-S bond cleavage and indicate that Arg-56, His-123, and Cys-364 are critical SufS residues in this C-S bond cleavage pathway.

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“…(1 mM) reduces the Schiff-base between the protein and PLP, resulting in a noticeable reduction in absorbance at 425 nm (Soniya and Chandra, 2018;Toney, 2011). Treatment of as-purified LpThi5…”

Section: Primer Name Sequencementioning

confidence: 99%

Functional characterization of the HMP‐P synthase of Legionella pneumophila (Lpg1565)

Paxhia

Swanson

Downs

2020

Molecular Microbiology

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Thiamine pyrophosphate (TPP), the active form of Vitamin B 1 , is a cofactor important for several enzymes in central metabolism including transketolase, pyruvate dehydrogenase, and α-ketoglutarate dehydrogenase. The cofactor is comprised of two moieties, 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate (HMP-PP) and 4-methyl-5-β-hydroxyethylthiazole phosphate (THZ-P), that are independently synthesized and combined to form TPP (Jurgenson et al., 2009). The pyrimidine precursor HMP-P is synthesized from an intermediate in the purine biosynthetic pathway (aminoimidazole ribotide) by the phosphomethylpyrimidine synthase ThiC (E.C. 4.1.99.17) an enzyme encoded in plants, archaea, and most bacteria (Jurgenson et al., 2009). However, some organisms, notably Saccharomyces cerevisiae, use Thi5 (HMP-P synthase) in place of ThiC to generate HMP-P. Labeling studies showed that the atoms of

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Free energy landscapes of prototropic tautomerism in pyridoxal 5′‐phosphate schiff bases at the active site of an enzyme in aqueous medium

Cited by 13 publications

References 53 publications

Free Energy Landscape and Proton Transfer Pathways of the Transimination Reaction at the Active site of the Serine Hydroxymethyltransferase Enzyme in Aqueous Medium

Free Energy Landscape and Proton Transfer Pathways of the Transimination Reaction at the Active site of the Serine Hydroxymethyltransferase Enzyme in Aqueous Medium

Direct observation of intermediates in the SufS cysteine desulfurase reaction reveals functional roles of conserved active-site residues

Functional characterization of the HMP‐P synthase of Legionella pneumophila (Lpg1565)

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