The crystal structure and catalytic mechanism of hydroxynitrile lyase from passion fruit, Passiflora edulis.
Identifieur interne : 000C39 ( Main/Exploration ); précédent : 000C38; suivant : 000C40The crystal structure and catalytic mechanism of hydroxynitrile lyase from passion fruit, Passiflora edulis.
Auteurs : Fumihiro Motojima [Japon] ; Aem Nuylert [Japon] ; Yasuhisa Asano [Japon]Source :
- The FEBS journal [ 1742-4658 ] ; 2018.
Descripteurs français
- KwdFr :
- Aldehyde-lyases (composition chimique), Aldehyde-lyases (génétique), Aldehyde-lyases (métabolisme), Catalyse (MeSH), Conformation des protéines (MeSH), Cristallographie aux rayons X (MeSH), Liaison hydrogène (MeSH), Modèles moléculaires (MeSH), Mutation (MeSH), Passiflora (enzymologie), Protéines végétales (composition chimique), Protéines végétales (génétique), Protéines végétales (métabolisme), Similitude de séquences d'acides aminés (MeSH), Séquence d'acides aminés (MeSH).
- MESH :
- composition chimique : Aldehyde-lyases, Protéines végétales.
- enzymologie : Passiflora.
- génétique : Aldehyde-lyases, Protéines végétales.
- métabolisme : Aldehyde-lyases, Protéines végétales.
- Catalyse, Conformation des protéines, Cristallographie aux rayons X, Liaison hydrogène, Modèles moléculaires, Mutation, Similitude de séquences d'acides aminés, Séquence d'acides aminés.
English descriptors
- KwdEn :
- Aldehyde-Lyases (chemistry), Aldehyde-Lyases (genetics), Aldehyde-Lyases (metabolism), Amino Acid Sequence (MeSH), Catalysis (MeSH), Crystallography, X-Ray (MeSH), Hydrogen Bonding (MeSH), Models, Molecular (MeSH), Mutation (MeSH), Passiflora (enzymology), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Protein Conformation (MeSH), Sequence Homology, Amino Acid (MeSH).
- MESH :
- chemical , chemistry : Aldehyde-Lyases, Plant Proteins.
- chemical , genetics : Aldehyde-Lyases, Plant Proteins.
- chemical , metabolism : Aldehyde-Lyases, Plant Proteins.
- enzymology : Passiflora.
- Amino Acid Sequence, Catalysis, Crystallography, X-Ray, Hydrogen Bonding, Models, Molecular, Mutation, Protein Conformation, Sequence Homology, Amino Acid.
Abstract
Hydroxynitrile lyases (HNLs) are enzymes used in the synthesis of chiral cyanohydrins. The HNL from Passiflora edulis (PeHNL) is R-selective and is the smallest HNL known to date. The crystal structures of PeHNL and its C-terminal peptide depleted derivative were determined by molecular replacement method using the template structure of a heat stable protein, SP1, from Populus tremula at 2.8 and 1.8 Å resolution, respectively. PeHNL belongs to dimeric α+β barrel superfamily consisting of a central β-barrel in the middle of a dimer. The structure of PeHNL complexed with (R)-mandelonitrile ((R)-MAN) was also determined. The hydroxyl group of (R)-MAN forms hydrogen bonds with His8 and Tyr30 in the active site, whereas the nitrile group is oriented toward the carboxyl group of Glu54, unlike other HNLs, where it interacts with basic residues typically. The results of mutational analysis indicate that the catalytic dyad of His8-Asn101 is critical for the enzymatic reaction. The length of the hydrogen bond between His-Nδ1 and Asn101-Oδ1 is short in the PeHNL-(R)-MAN complex (~ 2.6 Å), which would increase the basicity of His8 to abstract a proton from the hydroxyl group of (R)-MAN. The cyanide ion released from the nitrile group abstracts a proton from the protonated His8 to generate a hydrogen cyanide. Thus, the His8 in the active site of PeHNL acts both as a general acid and a general base in the reaction.
ENZYMES
EC 4.1.2.10 DATABASE: Structural data are available in PDB database under the accession numbers 5XZQ, 5XZT, and 5Y02.
DOI: 10.1111/febs.14339
PubMed: 29155493
Affiliations:
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xml:lang="fr">Japon</country><wicri:regionArea>Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu</wicri:regionArea><wicri:noRegion>Imizu</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Asano Active Enzyme Molecule Project, ERATO, JST, Imizu</wicri:regionArea><wicri:noRegion>Imizu</wicri:noRegion></affiliation></author></analytic><series><title level="j">The FEBS journal</title><idno type="eISSN">1742-4658</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Aldehyde-Lyases (chemistry)</term><term>Aldehyde-Lyases (genetics)</term><term>Aldehyde-Lyases (metabolism)</term><term>Amino Acid Sequence (MeSH)</term><term>Catalysis (MeSH)</term><term>Crystallography, X-Ray (MeSH)</term><term>Hydrogen Bonding (MeSH)</term><term>Models, Molecular (MeSH)</term><term>Mutation (MeSH)</term><term>Passiflora (enzymology)</term><term>Plant Proteins (chemistry)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Protein Conformation (MeSH)</term><term>Sequence Homology, Amino Acid (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Aldehyde-lyases (composition chimique)</term><term>Aldehyde-lyases (génétique)</term><term>Aldehyde-lyases (métabolisme)</term><term>Catalyse (MeSH)</term><term>Conformation des protéines (MeSH)</term><term>Cristallographie aux rayons X (MeSH)</term><term>Liaison hydrogène (MeSH)</term><term>Modèles moléculaires (MeSH)</term><term>Mutation (MeSH)</term><term>Passiflora (enzymologie)</term><term>Protéines végétales (composition chimique)</term><term>Protéines végétales (génétique)</term><term>Protéines végétales (métabolisme)</term><term>Similitude de séquences d'acides aminés (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Aldehyde-Lyases</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Aldehyde-Lyases</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Aldehyde-Lyases</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Aldehyde-lyases</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Passiflora</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Passiflora</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Aldehyde-lyases</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Aldehyde-lyases</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Catalysis</term><term>Crystallography, X-Ray</term><term>Hydrogen Bonding</term><term>Models, Molecular</term><term>Mutation</term><term>Protein Conformation</term><term>Sequence Homology, Amino Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Catalyse</term><term>Conformation des protéines</term><term>Cristallographie aux rayons X</term><term>Liaison hydrogène</term><term>Modèles moléculaires</term><term>Mutation</term><term>Similitude de séquences d'acides aminés</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Hydroxynitrile lyases (HNLs) are enzymes used in the synthesis of chiral cyanohydrins. The HNL from Passiflora edulis (PeHNL) is R-selective and is the smallest HNL known to date. The crystal structures of PeHNL and its C-terminal peptide depleted derivative were determined by molecular replacement method using the template structure of a heat stable protein, SP1, from Populus tremula at 2.8 and 1.8 Å resolution, respectively. PeHNL belongs to dimeric α+β barrel superfamily consisting of a central β-barrel in the middle of a dimer. The structure of PeHNL complexed with (R)-mandelonitrile ((R)-MAN) was also determined. The hydroxyl group of (R)-MAN forms hydrogen bonds with His8 and Tyr30 in the active site, whereas the nitrile group is oriented toward the carboxyl group of Glu54, unlike other HNLs, where it interacts with basic residues typically. The results of mutational analysis indicate that the catalytic dyad of His8-Asn101 is critical for the enzymatic reaction. The length of the hydrogen bond between His-Nδ1 and Asn101-Oδ1 is short in the PeHNL-(R)-MAN complex (~ 2.6 Å), which would increase the basicity of His8 to abstract a proton from the hydroxyl group of (R)-MAN. The cyanide ion released from the nitrile group abstracts a proton from the protonated His8 to generate a hydrogen cyanide. Thus, the His8 in the active site of PeHNL acts both as a general acid and a general base in the reaction.</div><div type="abstract" xml:lang="en"><p><b>ENZYMES</b></p><p>EC 4.1.2.10 DATABASE: Structural data are available in PDB database under the accession numbers 5XZQ, 5XZT, and 5Y02.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29155493</PMID><DateCompleted><Year>2018</Year><Month>12</Month><Day>11</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>11</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1742-4658</ISSN><JournalIssue CitedMedium="Internet"><Volume>285</Volume><Issue>2</Issue><PubDate><Year>2018</Year><Month>01</Month></PubDate></JournalIssue><Title>The FEBS journal</Title><ISOAbbreviation>FEBS J</ISOAbbreviation></Journal><ArticleTitle>The crystal structure and catalytic mechanism of hydroxynitrile lyase from passion fruit, Passiflora edulis.</ArticleTitle><Pagination><MedlinePgn>313-324</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/febs.14339</ELocationID><Abstract><AbstractText>Hydroxynitrile lyases (HNLs) are enzymes used in the synthesis of chiral cyanohydrins. The HNL from Passiflora edulis (PeHNL) is R-selective and is the smallest HNL known to date. The crystal structures of PeHNL and its C-terminal peptide depleted derivative were determined by molecular replacement method using the template structure of a heat stable protein, SP1, from Populus tremula at 2.8 and 1.8 Å resolution, respectively. PeHNL belongs to dimeric α+β barrel superfamily consisting of a central β-barrel in the middle of a dimer. The structure of PeHNL complexed with (R)-mandelonitrile ((R)-MAN) was also determined. The hydroxyl group of (R)-MAN forms hydrogen bonds with His8 and Tyr30 in the active site, whereas the nitrile group is oriented toward the carboxyl group of Glu54, unlike other HNLs, where it interacts with basic residues typically. The results of mutational analysis indicate that the catalytic dyad of His8-Asn101 is critical for the enzymatic reaction. The length of the hydrogen bond between His-Nδ1 and Asn101-Oδ1 is short in the PeHNL-(R)-MAN complex (~ 2.6 Å), which would increase the basicity of His8 to abstract a proton from the hydroxyl group of (R)-MAN. The cyanide ion released from the nitrile group abstracts a proton from the protonated His8 to generate a hydrogen cyanide. Thus, the His8 in the active site of PeHNL acts both as a general acid and a general base in the reaction.</AbstractText><AbstractText Label="ENZYMES">EC 4.1.2.10 DATABASE: Structural data are available in PDB database under the accession numbers 5XZQ, 5XZT, and 5Y02.</AbstractText><CopyrightInformation>© 2017 The Authors. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Motojima</LastName><ForeName>Fumihiro</ForeName><Initials>F</Initials><Identifier Source="ORCID">0000-0003-4461-8673</Identifier><AffiliationInfo><Affiliation>Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nuylert</LastName><ForeName>Aem</ForeName><Initials>A</Initials><Identifier Source="ORCID">0000-0002-8312-9592</Identifier><AffiliationInfo><Affiliation>Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Asano</LastName><ForeName>Yasuhisa</ForeName><Initials>Y</Initials><Identifier Source="ORCID">0000-0003-3645-3952</Identifier><AffiliationInfo><Affiliation>Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Japan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Asano Active Enzyme Molecule Project, ERATO, JST, Imizu, Japan.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>12</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>FEBS J</MedlineTA><NlmUniqueID>101229646</NlmUniqueID><ISSNLinking>1742-464X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 4.1.2.-</RegistryNumber><NameOfSubstance UI="D000446">Aldehyde-Lyases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 4.1.2.10</RegistryNumber><NameOfSubstance UI="C021541">mandelonitrile lyase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000446" MajorTopicYN="N">Aldehyde-Lyases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002384" MajorTopicYN="N">Catalysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018360" MajorTopicYN="N">Crystallography, X-Ray</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006860" MajorTopicYN="N">Hydrogen Bonding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="N">Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D029598" MajorTopicYN="N">Passiflora</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011487" MajorTopicYN="N">Protein Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017386" MajorTopicYN="N">Sequence Homology, Amino Acid</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Passiflora edulis
</Keyword><Keyword MajorTopicYN="Y">catalytic mechanism</Keyword><Keyword MajorTopicYN="Y">crystal structure</Keyword><Keyword MajorTopicYN="Y">dimeric α+β barrel</Keyword><Keyword MajorTopicYN="Y">hydroxynitrile lyase</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>07</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>10</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>11</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>11</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>12</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>11</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29155493</ArticleId><ArticleId IdType="doi">10.1111/febs.14339</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Japon</li></country></list><tree><country name="Japon"><noRegion><name sortKey="Motojima, Fumihiro" sort="Motojima, Fumihiro" uniqKey="Motojima F" first="Fumihiro" last="Motojima">Fumihiro Motojima</name></noRegion><name sortKey="Asano, Yasuhisa" sort="Asano, Yasuhisa" uniqKey="Asano Y" first="Yasuhisa" last="Asano">Yasuhisa Asano</name><name sortKey="Asano, Yasuhisa" sort="Asano, Yasuhisa" uniqKey="Asano Y" first="Yasuhisa" last="Asano">Yasuhisa Asano</name><name sortKey="Motojima, Fumihiro" sort="Motojima, Fumihiro" uniqKey="Motojima F" first="Fumihiro" last="Motojima">Fumihiro Motojima</name><name sortKey="Nuylert, Aem" sort="Nuylert, Aem" uniqKey="Nuylert A" first="Aem" last="Nuylert">Aem Nuylert</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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