Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization

Wang, Nan; Jiang, Jiahong; Li, Xichen; Tan, Hongwei; Zheng, Jimin; Chen, Guangju; Jia, Zongchao

doi:10.1371/journal.pone.0134879

Cited by 7 publications

(6 citation statements)

References 24 publications

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“…Although the mode of dimerization is different for YjjX (PDB code: 1U5W), Mj0226 (PDB code: 1B78), and Maf (PDB code: 1EXC) possibly because of different substrate specificities, the overall structures of the monomers are very similar. All the three proteins are nucleotide binding proteins . Comparison of their active sites, suggested that there is similar loop in all proteins, which might possibly play an important role in nucleotide binding …”

Section: Resultsmentioning

confidence: 98%

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Identification of a new nucleotide binding site by structural alignment and site directed mutagenesis

et al. 2018

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Nucleotide binding proteins are involved in many important cellular processes and form one of the largest protein families. Traditionally, the identification of nucleotide binding motif, such as the ATP binding P-loop, has relied on the comparison of protein sequences, consideration of the function of each of the proteins and the identification of signature motifs within the sequence. Sometimes, it is difficult to identify nucleotide binding proteins based on sequence alignment because of increased evolutionary distances. In such cases, structural alignments can provide a better guide for comparing specific features of sequences because the overall structures of these motifs are conserved despite low sequence identity. In the present study, on the basis of bioinformatics and structural comparison of three representative protein structures of Ham1 superfamily, YjjX, YggV, and YhdE, previously identified as nucleotide binding proteins, we have identified a novel nucleotide binding motif (T/SXXXXK/R). The importance of this signature motif in binding of nucleotides was validated using site directed mutagenesis. Mutations of conserved residues of the loop either decreased or completely abolished the nucleotide binding activity of the protein. We used the conserved motif identified in the study to search for other proteins having a similar motif. Two proteins, GTP cyclohydrolase II and dephospho-CoA pyrophosphorylase showed presence of the loop, suggesting that this nucleotide binding motif is not unique in the Ham1 superfamily, but represents a novel NTP recognition motif.

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Section: Resultsmentioning

confidence: 98%

“…All the three proteins are nucleotide binding proteins . Comparison of their active sites, suggested that there is similar loop in all proteins, which might possibly play an important role in nucleotide binding …”

Section: Resultsmentioning

confidence: 98%

Identification of a new nucleotide binding site by structural alignment and site directed mutagenesis

et al. 2018

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“…Enzymatic analysis by PPi fluorescence sensor shows the apparent K m of YhdE_E33A with dTTP is similar to that of wild-type YhdE, which indicates that Glu33 is probably not directly involved in dTTP binding. To help understand the hydrolysis mechanism of YhdE, we previously crystallized YhdE_E33A in the absence and presence of dTTP through co-crystallization 6 , 30 . Unfortunately, dTTP was not found in the YhdE_E33A structure from the co-crystallization, which is now not surprising because of the residual weak activity seen using our new PPi probe.…”

Section: Resultsmentioning

confidence: 99%

“…YhdE and its mutant were expressed and purified as described before 6 , 30 . The crystallization condition of the YhdE_E33A mutant included 0.1 M Tris (pH 8.0), 27% PEG 2000 MME and crystals were grown at 291 K for about two weeks.…”

Section: Methodsmentioning

confidence: 99%

A new method to investigate the catalytic mechanism of YhdE pyrophosphatase by using a pyrophosphate fluorescence probe

Shen

Tan

Xing

et al. 2017

Sci Rep

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YhdE is a Maf (multicopy associated filamentation) proteins from Escherichia coli which exhibits pyrophosphatase activity towards selected nucleotides, although its catalytic mechanism remains unclear. Herein we used a novel fluorescence probe (4-isoACBA–Zn(II) complex) to characterize the enzymatic properties of YhdE and its mutant, establishing a new method for assaying pyrophosphatase catalytic function. Our results reveal for the first time that the new fluorescence sensor confers high sensitivity and specificity and pyrophosphate (PPi) is the direct catalytic product of YhdE. Crystal structures of a mutant in the active-site loop (YhdE_E33A) show conformational flexibility implicated in the catalytic mechanism of YhdE. ITC experiments and computational docking further reveal that Asp70 and substrate dTTP coordinate Mn2+. Quantum mechanics calculations indicate that YhdE hydrolysis appears to follow a stepwise pathway in which a water molecule first attacks the α-phosphorus atom in the substrate, followed by the release of PPi from the pentavalent intermediate.

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“…34,53 For the binding free energies, it is made up by molecular mechanics (MM), electrostatic contributions to solvation, and nonpolar contributions to solvation. 54 In this process, the binding free energy of protein-ligand in the solvent was computed as:…”

Section: Binding Free Energiesmentioning

confidence: 99%

Exploring the effect of inhibitor AKB‐9778 on VE‐PTP by molecular docking and molecular dynamics simulation

Liu

Wang

Sun

et al. 2019

J of Cellular Biochemistry

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Diabetic macular edema, also known as diabetic eye disease, is mainly caused by the overexpression of vascular endothelial protein tyrosine phosphatase (VE‐PTP) at hypoxia/ischemic. AKB‐9778 is a known VE‐PTP inhibitor that can effectively interact with the active site of VE‐PTP to inhibit the activity of VE‐PTP. However, the binding pattern of VE‐PTP with AKB‐9778 and the dynamic implications of AKB‐9778 on VE‐PTP system at the molecular level are poorly understood. Through molecular docking, it was found that the AKB‐9778 was docked well in the binding pocket of VE‐PTP by the interactions of hydrogen bond and Van der Waals. Furthermore, after molecular dynamic simulations on VE‐PTP system and VE‐PTP AKB‐9778 system, a series of postdynamic analyses found that the flexibility and conformation of the active site undergone an obvious transition after VE‐PTP binding with AKB‐9778. Moreover, by constructing the RIN, it was found that the different interactions in the active site were the detailed reasons for the conformational differences between these two systems. Thus, the finding here might provide a deeper understanding of AKB‐9778 as VE‐PTP Inhibitor.

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Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization

Cited by 7 publications

References 24 publications

Identification of a new nucleotide binding site by structural alignment and site directed mutagenesis

Identification of a new nucleotide binding site by structural alignment and site directed mutagenesis

A new method to investigate the catalytic mechanism of YhdE pyrophosphatase by using a pyrophosphate fluorescence probe

Exploring the effect of inhibitor AKB‐9778 on VE‐PTP by molecular docking and molecular dynamics simulation

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