Structure-function relationship between soluble epoxide hydrolases structure and their tunnel network

Mitusińska, Karolina; Wojsa, Piotr; Bzówka, Maria; Raczyńska, Agata; Bagrowska, Weronika; Samol, Aleksandra; Kapica, Patryk; Góra, Artur

doi:10.1016/j.csbj.2021.10.042

Cited by 8 publications

(28 citation statements)

References 84 publications

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“…As we pointed out elsewhere(47) the Tc/m tunnel whose mouth is located between the main and cap domains can be seen as an ancestral tunnel created during cap domain insertion and preserved in nearly all epoxide hydrolases. In hsEH this tunnel ( Figure 5 , panel A ) has an average length of ∼13.3 Å.…”

Section: Resultsmentioning

confidence: 65%

“…The entropy values of the tunnel-lining residues are presented in Supplementary Table S13. As we pointed out elsewhere (47) the Tc/m tunnel whose mouth is located between the main and cap domains can be seen as an ancestral tunnel created during cap domain insertion and preserved in nearly all epoxide hydrolases. In hsEH this tunnel (Figure 5 Å, reaching a maximum of 2.7 Å.…”

Section: Detailed Analysis Of Selected Tunnelsmentioning

confidence: 71%

“…Those tunnels were then compared with the tunnels identified during MD simulations to find their corresponding counterparts ( Supplementary Table S3 ), based on the similarity of their tunnel-lining residues (for more details see the Methods section). We marked all identified tunnels according to their localisation within the epoxide hydrolase’s domains as was shown in our previous work(47). We identified tunnels passing through three regions of the sEH structure: i) the main domain (marked as Tg, Tm, Tback, and Tside), ii) the cap domain (marked as Tcap), as well as iii) the border between the cap and main domains (marked as Tc/m).…”

Section: Resultsmentioning

confidence: 99%

“…Members of this superfamily share a barrel-like scaffold of eight anti-parallel β-strands surrounded by α-helices with a mostly helical cap domain sitting on top of the entrance to the active site (45), which seems to be also the oldest(51) and most stable( 52) fold used by one the largest groups of enzymes (53). Structural and evolutionary analyses of EHs have been reported systematically (40,47,(54)(55)(56), providing valuable insights into their structural and functional features. In our work, we first assessed the system-specific compartments described previously by Barth et al, such as the main and cap domains, the NC-loop, and the cap-loop, along with secondary structure elements such as strands, helices, and loops.…”

Section: Discussionmentioning

confidence: 99%

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Evolution of tunnels in α/β-hydrolase fold proteins – what can we learn from studying epoxide hydrolases?

Bzówka

Mitusińska

Raczyńska

et al. 2021

Preprint

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The evolutionary variability of a protein's residues is highly dependent on protein region and protein function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried residues. Active site residues are considered to be conserved as they ensure an enzyme's activity and selectivity. The abovementioned rules apply also to α/β-hydrolase fold proteins - an example of enzymes with buried active sites equipped with tunnels linking the reaction site with the exterior. We hypothesised two scenarios: (1) tunnels are lined by mostly variable residues, allowing adaptation to the evolutionary pressures of a changeable environment; or (2) tunnels are lined by mostly conserved amino acids, and are equipped with a number of specific variable residues that are able to respond to evolutionary pressure. We also wanted to check if evolutionary analysis can help distinguish functional and non-functional tunnels. Soluble epoxide hydrolases (sEHs) represent a good case study for the analysis of the evolution of tunnels in an α/β-hydrolase fold family due to their size and architecture. Here, we propose methods for the comparison of tunnels detected in both crystal structures and molecular dynamics simulations, as well as the assignment of tunnel functionality, and we identify critical steps for careful tunnel inspection. We also compare the entropy values of the tunnel-lining residues and system-specific compartments in seven selected sEHs from different clades. We present three different cases of entropy distribution among tunnel-lining residues. As a result, we propose a 'perforation' model for tunnel evolution via the merging of internal cavities or surface perforations. We also report an approach for the identification of highly variable tunnel-lining residues as potential targets to be used for the fine-tuning of selected enzymes.

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Section: Resultsmentioning

confidence: 65%

Section: Detailed Analysis Of Selected Tunnelsmentioning

confidence: 71%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Evolution of tunnels in α/β-hydrolase fold proteins – what can we learn from studying epoxide hydrolases?

Bzówka

Mitusińska

Raczyńska

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Those tunnels were then compared with the tunnels identified during MD simulations to find their corresponding counterparts (S3 Table ), based on the similarity of their tunnel-lining residues (for more details see the Methods section). We marked all identified tunnels according to their localisation within the epoxide hydrolase's domains as was shown in our previous work [47]. We identified tunnels passing through three regions of the sEH structure: i) the main domain (marked as Tg, Tm, Tback, and Tside), ii) the cap domain (marked as Tcap), as well as iii) the border between the cap and main domains (marked as Tc/m).…”

Section: Tunnel Identification and Comparisonmentioning

confidence: 99%

Evolution of tunnels in α/β-hydrolase fold proteins—What can we learn from studying epoxide hydrolases?

et al. 2022

Self Cite

View full text Add to dashboard Cite

The evolutionary variability of a protein’s residues is highly dependent on protein region and function. Solvent-exposed residues, excluding those at interaction interfaces, are more variable than buried residues whereas active site residues are considered to be conserved. The abovementioned rules apply also to α/β-hydrolase fold proteins—one of the oldest and the biggest superfamily of enzymes with buried active sites equipped with tunnels linking the reaction site with the exterior. We selected soluble epoxide hydrolases as representative of this family to conduct the first systematic study on the evolution of tunnels. We hypothesised that tunnels are lined by mostly conserved residues, and are equipped with a number of specific variable residues that are able to respond to evolutionary pressure. The hypothesis was confirmed, and we suggested a general and detailed way of the tunnels’ evolution analysis based on entropy values calculated for tunnels’ residues. We also found three different cases of entropy distribution among tunnel-lining residues. These observations can be applied for protein reengineering mimicking the natural evolution process. We propose a ‘perforation’ mechanism for new tunnels design via the merging of internal cavities or protein surface perforation. Based on the literature data, such a strategy of new tunnel design could significantly improve the enzyme’s performance and can be applied widely for enzymes with buried active sites.

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Essential amino acid residues and catalytic mechanism of trans-epoxysuccinate hydrolase for production of meso-tartaric acid

Liao,

Pan,

Yao

et al. 2024

Biotechnol Lett

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This study aimed to discuss the essential amino acid residues and catalytic mechanism of transepoxycussinate hydrolase from Pseudomonas koreensis for production of meso-tartaric acid. ResultsThe optimum conditions of the enzyme were 45°C and pH 9.0, respectively. It was strongly inhibited by Zn 2+ , Mn 2+ and SDS. Michaelis-Menten enzyme kinetics analysis gave a K m value of 3.50 mM and a k cat of 99.75 s − 1 , the EE value was higher than 99.9%. Multiple sequence alignment and homology modeling showed that the enzyme belonged to MhpC superfamily and had a typical α/β hydrolase folding structure. Site-directed mutagenesis indicated H34,

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Structure-function relationship between soluble epoxide hydrolases structure and their tunnel network

Abstract: Graphical abstract

Cited by 8 publications

References 84 publications

Evolution of tunnels in α/β-hydrolase fold proteins – what can we learn from studying epoxide hydrolases?

Evolution of tunnels in α/β-hydrolase fold proteins – what can we learn from studying epoxide hydrolases?

Evolution of tunnels in α/β-hydrolase fold proteins—What can we learn from studying epoxide hydrolases?

Essential amino acid residues and catalytic mechanism of trans-epoxysuccinate hydrolase for production of meso-tartaric acid

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