Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis
Geraniol degradation pathway has long been elucidated in microorganisms through bioconversion studies, yet weakly characterised in plants; enzyme with specific nerol-oxidising activity has not been reported. A novel cDNA encodes nerol dehydrogenase (PmNeDH) was isolated from Persicaria minor. The re...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2018
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| Online Access: | http://psasir.upm.edu.my/id/eprint/73982/ http://psasir.upm.edu.my/id/eprint/73982/1/Structural%20and%20kinetic%20studies%20of%20a%20novel%20nerol%20dehydrogenase%20from%20Persicaria%20minor%2C%20a%20nerol-specific%20enzyme%20for%20citral%20biosynthesis.pdf |
| _version_ | 1848857409355776000 |
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| author | Tan, Cheng Seng Hassan, Maizom Mohamed Hussein, Zeti Azura Ismail, Ismanizan Ho, Kok Lian Ng, Chyan Leong Zainal, Zamri |
| author_facet | Tan, Cheng Seng Hassan, Maizom Mohamed Hussein, Zeti Azura Ismail, Ismanizan Ho, Kok Lian Ng, Chyan Leong Zainal, Zamri |
| author_sort | Tan, Cheng Seng |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Geraniol degradation pathway has long been elucidated in microorganisms through bioconversion studies, yet weakly characterised in plants; enzyme with specific nerol-oxidising activity has not been reported. A novel cDNA encodes nerol dehydrogenase (PmNeDH) was isolated from Persicaria minor. The recombinant PmNeDH (rPmNeDH) is a homodimeric enzyme that belongs to MDR (medium-chain dehydrogenases/reductases) superfamily that catalyses the first oxidative step of geraniol degradation pathway in citral biosynthesis. Kinetic analysis revealed that rPmNeDH has a high specificity for allylic primary alcohols with backbone ≤10 carbons. rPmNeDH has ∼3 fold higher affinity towards nerol (cis-3,7-dimethyl-2,6-octadien-1-ol) than its trans-isomer, geraniol. To our knowledge, this is the first alcohol dehydrogenase with higher preference towards nerol, suggesting that nerol can be effective substrate for citral biosynthesis in P. minor. The rPmNeDH crystal structure (1.54 Å) showed high similarity with enzyme structures from MDR superfamily. Structure guided mutation was conducted to describe the relationships between substrate specificity and residue substitutions in the active site. Kinetics analyses of wild-type rPmNeDH and several active site mutants demonstrated that the substrate specificity of rPmNeDH can be altered by changing any selected active site residues (Asp280, Leu294 and Ala303). Interestingly, the L294F, A303F and A303G mutants were able to revamp the substrate preference towards geraniol. Furthermore, mutant that exhibited a broader substrate range was also obtained. This study demonstrates that P. minor may have evolved to contain enzyme that optimally recognise cis-configured nerol as substrate. rPmNeDH structure provides new insights into the substrate specificity and active site plasticity in MDR superfamily. |
| first_indexed | 2025-11-15T11:57:05Z |
| format | Article |
| id | upm-73982 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T11:57:05Z |
| publishDate | 2018 |
| publisher | Elsevier |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-739822020-04-28T22:41:29Z http://psasir.upm.edu.my/id/eprint/73982/ Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis Tan, Cheng Seng Hassan, Maizom Mohamed Hussein, Zeti Azura Ismail, Ismanizan Ho, Kok Lian Ng, Chyan Leong Zainal, Zamri Geraniol degradation pathway has long been elucidated in microorganisms through bioconversion studies, yet weakly characterised in plants; enzyme with specific nerol-oxidising activity has not been reported. A novel cDNA encodes nerol dehydrogenase (PmNeDH) was isolated from Persicaria minor. The recombinant PmNeDH (rPmNeDH) is a homodimeric enzyme that belongs to MDR (medium-chain dehydrogenases/reductases) superfamily that catalyses the first oxidative step of geraniol degradation pathway in citral biosynthesis. Kinetic analysis revealed that rPmNeDH has a high specificity for allylic primary alcohols with backbone ≤10 carbons. rPmNeDH has ∼3 fold higher affinity towards nerol (cis-3,7-dimethyl-2,6-octadien-1-ol) than its trans-isomer, geraniol. To our knowledge, this is the first alcohol dehydrogenase with higher preference towards nerol, suggesting that nerol can be effective substrate for citral biosynthesis in P. minor. The rPmNeDH crystal structure (1.54 Å) showed high similarity with enzyme structures from MDR superfamily. Structure guided mutation was conducted to describe the relationships between substrate specificity and residue substitutions in the active site. Kinetics analyses of wild-type rPmNeDH and several active site mutants demonstrated that the substrate specificity of rPmNeDH can be altered by changing any selected active site residues (Asp280, Leu294 and Ala303). Interestingly, the L294F, A303F and A303G mutants were able to revamp the substrate preference towards geraniol. Furthermore, mutant that exhibited a broader substrate range was also obtained. This study demonstrates that P. minor may have evolved to contain enzyme that optimally recognise cis-configured nerol as substrate. rPmNeDH structure provides new insights into the substrate specificity and active site plasticity in MDR superfamily. Elsevier 2018 Article PeerReviewed text en http://psasir.upm.edu.my/id/eprint/73982/1/Structural%20and%20kinetic%20studies%20of%20a%20novel%20nerol%20dehydrogenase%20from%20Persicaria%20minor%2C%20a%20nerol-specific%20enzyme%20for%20citral%20biosynthesis.pdf Tan, Cheng Seng and Hassan, Maizom and Mohamed Hussein, Zeti Azura and Ismail, Ismanizan and Ho, Kok Lian and Ng, Chyan Leong and Zainal, Zamri (2018) Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis. Plant Physiology and Biochemistry, 123. 359 - 368. ISSN 0981-9428; ESSN: 1873-2690 https://www.ncbi.nlm.nih.gov/pubmed/29304481 10.1016/j.plaphy.2017.12.033 |
| spellingShingle | Tan, Cheng Seng Hassan, Maizom Mohamed Hussein, Zeti Azura Ismail, Ismanizan Ho, Kok Lian Ng, Chyan Leong Zainal, Zamri Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis |
| title | Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis |
| title_full | Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis |
| title_fullStr | Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis |
| title_full_unstemmed | Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis |
| title_short | Structural and kinetic studies of a novel nerol dehydrogenase from Persicaria minor, a nerol-specific enzyme for citral biosynthesis |
| title_sort | structural and kinetic studies of a novel nerol dehydrogenase from persicaria minor, a nerol-specific enzyme for citral biosynthesis |
| url | http://psasir.upm.edu.my/id/eprint/73982/ http://psasir.upm.edu.my/id/eprint/73982/ http://psasir.upm.edu.my/id/eprint/73982/ http://psasir.upm.edu.my/id/eprint/73982/1/Structural%20and%20kinetic%20studies%20of%20a%20novel%20nerol%20dehydrogenase%20from%20Persicaria%20minor%2C%20a%20nerol-specific%20enzyme%20for%20citral%20biosynthesis.pdf |