Crystallographic, kinetic, and spectroscopic study of the first ligninolytic peroxidase presenting a catalytic tyrosine.
Identifieur interne : 000517 ( Main/Exploration ); précédent : 000516; suivant : 000518Crystallographic, kinetic, and spectroscopic study of the first ligninolytic peroxidase presenting a catalytic tyrosine.
Auteurs : Yuta Miki [Espagne] ; Fabiola R. Calvi O ; Rebecca Pogni ; Stefania Giansanti ; Francisco J. Ruiz-Due As ; María Jesús Martínez ; Riccardo Basosi ; Antonio Romero ; Angel T. MartínezSource :
- The Journal of biological chemistry [ 1083-351X ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
- composition chimique : Peroxidases.
- enzymologie : Trametes.
- métabolisme : Tyrosine.
- Analyse spectrale, Biocatalyse, Cinétique, Cristallographie aux rayons X, Oxydoréduction, Électrons.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Peroxidases.
- enzymology : Trametes.
- chemical , metabolism : Tyrosine.
- Biocatalysis, Crystallography, X-Ray, Electrons, Kinetics, Oxidation-Reduction, Spectrum Analysis.
Abstract
Trametes cervina lignin peroxidase (LiP) is a unique enzyme lacking the catalytic tryptophan strictly conserved in all other LiPs and versatile peroxidases (more than 30 sequences available). Recombinant T. cervina LiP and site-directed variants were investigated by crystallographic, kinetic, and spectroscopic techniques. The crystal structure shows three substrate oxidation site candidates involving His-170, Asp-146, and Tyr-181. Steady-state kinetics for oxidation of veratryl alcohol (the typical LiP substrate) by variants at the above three residues reveals a crucial role of Tyr-181 in LiP activity. Moreover, assays with ferrocytochrome c show that its ability to oxidize large molecules (a requisite property for oxidation of the lignin polymer) originates in Tyr-181. This residue is also involved in the oxidation of 1,4-dimethoxybenzene, a reaction initiated by the one-electron abstraction with formation of substrate cation radical, as described for the well known Phanerochaete chrysosporium LiP. Detailed spectroscopic and kinetic investigations, including low temperature EPR, show that the porphyrin radical in the two-electron activated T. cervina LiP is unstable and rapidly receives one electron from Tyr-181, forming a catalytic protein radical, which is identified as an H-bonded neutral tyrosyl radical. The crystal structure reveals a partially exposed location of Tyr-181, compatible with its catalytic role, and several neighbor residues probably contributing to catalysis: (i) by enabling substrate recognition by aromatic interactions; (ii) by acting as proton acceptor/donor from Tyr-181 or H-bonding the radical form; and (iii) by providing the acidic environment that would facilitate oxidation. This is the first structure-function study of the only ligninolytic peroxidase described to date that has a catalytic tyrosine.
DOI: 10.1074/jbc.M111.220996
PubMed: 21367853
PubMed Central: PMC3083212
Affiliations:
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Ruiz-Due As</name></author><author><name sortKey="Martinez, Maria Jesus" sort="Martinez, Maria Jesus" uniqKey="Martinez M" first="María Jesús" last="Martínez">María Jesús Martínez</name></author><author><name sortKey="Basosi, Riccardo" sort="Basosi, Riccardo" uniqKey="Basosi R" first="Riccardo" last="Basosi">Riccardo Basosi</name></author><author><name sortKey="Romero, Antonio" sort="Romero, Antonio" uniqKey="Romero A" first="Antonio" last="Romero">Antonio Romero</name></author><author><name sortKey="Martinez, Angel T" sort="Martinez, Angel T" uniqKey="Martinez A" first="Angel T" last="Martínez">Angel T. Martínez</name></author></analytic><series><title level="j">The Journal of biological chemistry</title><idno type="eISSN">1083-351X</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biocatalysis (MeSH)</term><term>Crystallography, X-Ray (MeSH)</term><term>Electrons (MeSH)</term><term>Kinetics (MeSH)</term><term>Oxidation-Reduction (MeSH)</term><term>Peroxidases (chemistry)</term><term>Spectrum Analysis (MeSH)</term><term>Trametes (enzymology)</term><term>Tyrosine (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse spectrale (MeSH)</term><term>Biocatalyse (MeSH)</term><term>Cinétique (MeSH)</term><term>Cristallographie aux rayons X (MeSH)</term><term>Oxydoréduction (MeSH)</term><term>Peroxidases (composition chimique)</term><term>Trametes (enzymologie)</term><term>Tyrosine (métabolisme)</term><term>Électrons (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Peroxidases</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Peroxidases</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Trametes</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Trametes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Tyrosine</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Tyrosine</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biocatalysis</term><term>Crystallography, X-Ray</term><term>Electrons</term><term>Kinetics</term><term>Oxidation-Reduction</term><term>Spectrum Analysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse spectrale</term><term>Biocatalyse</term><term>Cinétique</term><term>Cristallographie aux rayons X</term><term>Oxydoréduction</term><term>Électrons</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Trametes cervina lignin peroxidase (LiP) is a unique enzyme lacking the catalytic tryptophan strictly conserved in all other LiPs and versatile peroxidases (more than 30 sequences available). Recombinant T. cervina LiP and site-directed variants were investigated by crystallographic, kinetic, and spectroscopic techniques. The crystal structure shows three substrate oxidation site candidates involving His-170, Asp-146, and Tyr-181. Steady-state kinetics for oxidation of veratryl alcohol (the typical LiP substrate) by variants at the above three residues reveals a crucial role of Tyr-181 in LiP activity. Moreover, assays with ferrocytochrome c show that its ability to oxidize large molecules (a requisite property for oxidation of the lignin polymer) originates in Tyr-181. This residue is also involved in the oxidation of 1,4-dimethoxybenzene, a reaction initiated by the one-electron abstraction with formation of substrate cation radical, as described for the well known Phanerochaete chrysosporium LiP. Detailed spectroscopic and kinetic investigations, including low temperature EPR, show that the porphyrin radical in the two-electron activated T. cervina LiP is unstable and rapidly receives one electron from Tyr-181, forming a catalytic protein radical, which is identified as an H-bonded neutral tyrosyl radical. The crystal structure reveals a partially exposed location of Tyr-181, compatible with its catalytic role, and several neighbor residues probably contributing to catalysis: (i) by enabling substrate recognition by aromatic interactions; (ii) by acting as proton acceptor/donor from Tyr-181 or H-bonding the radical form; and (iii) by providing the acidic environment that would facilitate oxidation. This is the first structure-function study of the only ligninolytic peroxidase described to date that has a catalytic tyrosine.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21367853</PMID><DateCompleted><Year>2011</Year><Month>07</Month><Day>14</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1083-351X</ISSN><JournalIssue CitedMedium="Internet"><Volume>286</Volume><Issue>17</Issue><PubDate><Year>2011</Year><Month>Apr</Month><Day>29</Day></PubDate></JournalIssue><Title>The Journal of biological chemistry</Title><ISOAbbreviation>J Biol Chem</ISOAbbreviation></Journal><ArticleTitle>Crystallographic, kinetic, and spectroscopic study of the first ligninolytic peroxidase presenting a catalytic tyrosine.</ArticleTitle><Pagination><MedlinePgn>15525-34</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1074/jbc.M111.220996</ELocationID><Abstract><AbstractText>Trametes cervina lignin peroxidase (LiP) is a unique enzyme lacking the catalytic tryptophan strictly conserved in all other LiPs and versatile peroxidases (more than 30 sequences available). Recombinant T. cervina LiP and site-directed variants were investigated by crystallographic, kinetic, and spectroscopic techniques. The crystal structure shows three substrate oxidation site candidates involving His-170, Asp-146, and Tyr-181. Steady-state kinetics for oxidation of veratryl alcohol (the typical LiP substrate) by variants at the above three residues reveals a crucial role of Tyr-181 in LiP activity. Moreover, assays with ferrocytochrome c show that its ability to oxidize large molecules (a requisite property for oxidation of the lignin polymer) originates in Tyr-181. This residue is also involved in the oxidation of 1,4-dimethoxybenzene, a reaction initiated by the one-electron abstraction with formation of substrate cation radical, as described for the well known Phanerochaete chrysosporium LiP. Detailed spectroscopic and kinetic investigations, including low temperature EPR, show that the porphyrin radical in the two-electron activated T. cervina LiP is unstable and rapidly receives one electron from Tyr-181, forming a catalytic protein radical, which is identified as an H-bonded neutral tyrosyl radical. The crystal structure reveals a partially exposed location of Tyr-181, compatible with its catalytic role, and several neighbor residues probably contributing to catalysis: (i) by enabling substrate recognition by aromatic interactions; (ii) by acting as proton acceptor/donor from Tyr-181 or H-bonding the radical form; and (iii) by providing the acidic environment that would facilitate oxidation. This is the first structure-function study of the only ligninolytic peroxidase described to date that has a catalytic tyrosine.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Miki</LastName><ForeName>Yuta</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, E-28040 Madrid, Spain.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Calviño</LastName><ForeName>Fabiola R</ForeName><Initials>FR</Initials></Author><Author ValidYN="Y"><LastName>Pogni</LastName><ForeName>Rebecca</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Giansanti</LastName><ForeName>Stefania</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Ruiz-Dueñas</LastName><ForeName>Francisco J</ForeName><Initials>FJ</Initials></Author><Author ValidYN="Y"><LastName>Martínez</LastName><ForeName>María Jesús</ForeName><Initials>MJ</Initials></Author><Author ValidYN="Y"><LastName>Basosi</LastName><ForeName>Riccardo</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Romero</LastName><ForeName>Antonio</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Martínez</LastName><ForeName>Angel T</ForeName><Initials>AT</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>PDB</DataBankName><AccessionNumberList><AccessionNumber>3Q3U</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>03</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Biol 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2009;60(2):441-52</Citation><ArticleIdList><ArticleId IdType="pubmed">18987391</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Espagne</li></country><region><li>Communauté de Madrid</li></region></list><tree><noCountry><name sortKey="Basosi, Riccardo" sort="Basosi, Riccardo" uniqKey="Basosi R" first="Riccardo" last="Basosi">Riccardo Basosi</name><name sortKey="Calvi O, Fabiola R" sort="Calvi O, Fabiola R" uniqKey="Calvi O F" first="Fabiola R" last="Calvi O">Fabiola R. Calvi O</name><name sortKey="Giansanti, Stefania" sort="Giansanti, Stefania" uniqKey="Giansanti S" first="Stefania" last="Giansanti">Stefania Giansanti</name><name sortKey="Martinez, Angel T" sort="Martinez, Angel T" uniqKey="Martinez A" first="Angel T" last="Martínez">Angel T. Martínez</name><name sortKey="Martinez, Maria Jesus" sort="Martinez, Maria Jesus" uniqKey="Martinez M" first="María Jesús" last="Martínez">María Jesús Martínez</name><name sortKey="Pogni, Rebecca" sort="Pogni, Rebecca" uniqKey="Pogni R" first="Rebecca" last="Pogni">Rebecca Pogni</name><name sortKey="Romero, Antonio" sort="Romero, Antonio" uniqKey="Romero A" first="Antonio" last="Romero">Antonio Romero</name><name sortKey="Ruiz Due As, Francisco J" sort="Ruiz Due As, Francisco J" uniqKey="Ruiz Due As F" first="Francisco J" last="Ruiz-Due As">Francisco J. Ruiz-Due As</name></noCountry><country name="Espagne"><region name="Communauté de Madrid"><name sortKey="Miki, Yuta" sort="Miki, Yuta" uniqKey="Miki Y" first="Yuta" last="Miki">Yuta Miki</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Crystallographic, kinetic, and spectroscopic study of the first ligninolytic peroxidase presenting a catalytic tyrosine.
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