Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4
PsEst3, a psychrophilic esterase obtained from Paenibacillus sp. R4, which was isolated from the permafrost of Alaska, exhibits relatively high activity at low temperatures. Here, crystal structures of PsEst3 complexed with various ligands were generated and studied at atomic resolution, and biochem...
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| Format: | Article |
| Language: | English |
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International Union of Crystallography
2023-03-01
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| Series: | IUCrJ |
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| Online Access: | http://scripts.iucr.org/cgi-bin/paper?S2052252523001562 |
| _version_ | 1811161218398814208 |
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| author | Jonghyeon Son Woong Choi Hyun Kim Minseo Kim Jun Hyuck Lee Seung Chul Shin Han-Woo Kim |
| author_facet | Jonghyeon Son Woong Choi Hyun Kim Minseo Kim Jun Hyuck Lee Seung Chul Shin Han-Woo Kim |
| author_sort | Jonghyeon Son |
| collection | DOAJ |
| description | PsEst3, a psychrophilic esterase obtained from Paenibacillus sp. R4, which was isolated from the permafrost of Alaska, exhibits relatively high activity at low temperatures. Here, crystal structures of PsEst3 complexed with various ligands were generated and studied at atomic resolution, and biochemical studies were performed to analyze the structure–function relationship of PsEst3. Certain unique characteristics of PsEst3 distinct from those of other classes of lipases/esterases were identified. Firstly, PsEst3 contains a conserved GHSRA/G pentapeptide sequence in the GxSxG motif around the nucleophilic serine. Additionally, it contains a conserved HGFR/K consensus sequence in the oxyanion hole, which is distinct from that in other lipase/esterase families, as well as a specific domain composition (for example a helix–turn–helix motif) and a degenerative lid domain that exposes the active site to the solvent. Secondly, the electrostatic potential of the active site in PsEst3 is positive, which may cause unintended binding of negatively charged chemicals in the active site. Thirdly, the last residue of the oxyanion hole-forming sequence, Arg44, separates the active site from the solvent by sealing the acyl-binding pocket, suggesting that PsEst3 is an enzyme that is customized to sense an unidentified substrate that is distinct from those of classical lipases/esterases. Collectively, this evidence strongly suggests that PsEst3 belongs to a distinct family of esterases. |
| first_indexed | 2024-04-10T06:10:47Z |
| format | Article |
| id | doaj.art-816bc15c034e4edfbd7031339c4521ed |
| institution | Directory Open Access Journal |
| issn | 2052-2525 |
| language | English |
| last_indexed | 2024-04-10T06:10:47Z |
| publishDate | 2023-03-01 |
| publisher | International Union of Crystallography |
| record_format | Article |
| series | IUCrJ |
| spelling | doaj.art-816bc15c034e4edfbd7031339c4521ed2023-03-02T16:45:21ZengInternational Union of CrystallographyIUCrJ2052-25252023-03-0110222023210.1107/S2052252523001562jt5064Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4Jonghyeon Son0Woong Choi1Hyun Kim2Minseo Kim3Jun Hyuck Lee4Seung Chul Shin5Han-Woo Kim6Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of KoreaResearch Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of KoreaResearch Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of KoreaResearch Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of KoreaResearch Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of KoreaDivision of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of KoreaResearch Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of KoreaPsEst3, a psychrophilic esterase obtained from Paenibacillus sp. R4, which was isolated from the permafrost of Alaska, exhibits relatively high activity at low temperatures. Here, crystal structures of PsEst3 complexed with various ligands were generated and studied at atomic resolution, and biochemical studies were performed to analyze the structure–function relationship of PsEst3. Certain unique characteristics of PsEst3 distinct from those of other classes of lipases/esterases were identified. Firstly, PsEst3 contains a conserved GHSRA/G pentapeptide sequence in the GxSxG motif around the nucleophilic serine. Additionally, it contains a conserved HGFR/K consensus sequence in the oxyanion hole, which is distinct from that in other lipase/esterase families, as well as a specific domain composition (for example a helix–turn–helix motif) and a degenerative lid domain that exposes the active site to the solvent. Secondly, the electrostatic potential of the active site in PsEst3 is positive, which may cause unintended binding of negatively charged chemicals in the active site. Thirdly, the last residue of the oxyanion hole-forming sequence, Arg44, separates the active site from the solvent by sealing the acyl-binding pocket, suggesting that PsEst3 is an enzyme that is customized to sense an unidentified substrate that is distinct from those of classical lipases/esterases. Collectively, this evidence strongly suggests that PsEst3 belongs to a distinct family of esterases.http://scripts.iucr.org/cgi-bin/paper?S2052252523001562x-ray crystallographyprotein structurestructure–function relationshipesterasesligand selectivityprotein engineeringstructure determinationenzyme mechanismspsest3paenibacillus sp. r4 |
| spellingShingle | Jonghyeon Son Woong Choi Hyun Kim Minseo Kim Jun Hyuck Lee Seung Chul Shin Han-Woo Kim Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4 IUCrJ x-ray crystallography protein structure structure–function relationship esterases ligand selectivity protein engineering structure determination enzyme mechanisms psest3 paenibacillus sp. r4 |
| title | Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4 |
| title_full | Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4 |
| title_fullStr | Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4 |
| title_full_unstemmed | Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4 |
| title_short | Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4 |
| title_sort | structural and biochemical insights into psest3 a new ghsr type esterase obtained from paenibacillus sp r4 |
| topic | x-ray crystallography protein structure structure–function relationship esterases ligand selectivity protein engineering structure determination enzyme mechanisms psest3 paenibacillus sp. r4 |
| url | http://scripts.iucr.org/cgi-bin/paper?S2052252523001562 |
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