Characterization of a putative metal-dependent PTP-like phosphatase from Lactobacillus helveticus 2126

TL;DR

This study characterizes a new metal-dependent phosphatase from Lactobacillus helveticus 2126, revealing its structure and activity for potential use in genetic engineering.

Contribution

The paper reports the characterization and structural modeling of a novel PTP-like phosphatase from a probiotic bacterium.

Findings

The phosphatase showed highest specificity for sodium phytate with a low Km value of 299.50 ± 4.95 μM.

The enzyme's activity was enhanced by zinc, magnesium, and manganese ions, indicating PTP-like behavior.

Homology modeling revealed a distorted TIM barrel structure with a trinuclear metal center and 90.9% favorable Ramachandran plot residues.

Abstract

To date, there are very limited reports on sequence analysis and structure-based molecular modeling of phosphatases produced by probiotic bacteria. Therefore, a novel protein tyrosine-like phosphatase was characterized from L. helveticus 2126 in this study. The purified bacterial phosphatase was subjected to mass spectrometric analysis, and the identity of constructed sequence was analyzed using peptide mass fingerprint. The 3-D structure of protein was elucidated using homology modeling, while its stability was assessed using Ramachandran plot, VERIFY 3D, and PROCHECK. The bacterium produced an extracellular phosphatase of zone diameter 15 ± 0.8 mm on screening medium within 24 h of incubation. This bacterial phosphatase was highly specific towards sodium phytate as it yielded the lowest Km value of 299.50 ± 4.95 μM compared to other phosphorylated substrates. The activity was effectively stimulated in the presence of zinc, magnesium, and manganese ions thereby showing its PTP-like behavior. The phosphatase showed a molecular mass of 43 kDa, and the corresponding M/Z ratio data yielded 46% query coverage to Bacillus subtilis (3QY7). This showed a 61.1% sequence similarity to Ligilactobacillus ruminis (WP_046923835.1). The final sequence construct based on these bacteria showed a conserved motif “HCHILPGIDD” in their active site. In addition, homology modeling showed a distorted Tim barrel structure with a trinuclear metal center. The final model after energy minimization showed 90.9% of the residues in the favorable region of Ramachandran’s plot. This structural information can be used in genetic engineering for improving the overall stability and catalytic efficiency of probiotic bacterial phosphatases.

The online version contains supplementary material available at 10.1007/s10123-023-00390-w.

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