Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members.
Identifieur interne : 000101 ( Main/Exploration ); précédent : 000100; suivant : 000102Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members.
Auteurs : Andre S. Godoy [Brésil] ; Caroline S. Pereira [Brésil] ; Marina Paglione Ramia [Brésil] ; Rodrigo L. Silveira [Brésil] ; Cesar M. Camilo [Brésil] ; Marco A. Kadowaki [Brésil] ; Lene Lange [Danemark] ; Peter K. Busk [Danemark] ; Alessandro S. Nascimento [Brésil] ; Munir S. Skaf [Brésil] ; Igor Polikarpov [Brésil]Source :
- Scientific reports [ 2045-2322 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- composition chimique : Cellulase.
- enzymologie : Phanerochaete.
- métabolisme : Cellulase.
- Biologie informatique, Catalyse, Cristallographie aux rayons X, Dosages enzymatiques, Simulation de dynamique moléculaire.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Cellulase.
- chemical , metabolism : Cellulase.
- enzymology : Phanerochaete.
- Catalysis, Computational Biology, Crystallography, X-Ray, Enzyme Assays, Molecular Dynamics Simulation.
Abstract
The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of β-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general architecture, substrate binding and cleavage. Here, we use a combination of X-ray crystallography, bioinformatics, enzymatic assays, molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure, substrate binding and enzymatic specificity of the GH45 subfamily C endoglucanase from Phanerochaete chrysosporium (PcCel45A). We investigated the role played by different residues in the binding of the enzyme to cellulose oligomers of different lengths and examined the structural characteristics and dynamics of PcCel45A that make subfamily C so dissimilar to other members of the GH45 family. Due to the structural similarity shared between PcCel45A and domain I of expansins, comparative analysis of their substrate binding was also carried out. Our bioinformatics sequence analyses revealed that the hydrolysis mechanisms in GH45 subfamily C is not restricted to use of the imidic asparagine as a general base in the "Newton's cradle" catalytic mechanism recently proposed for this subfamily.
DOI: 10.1038/s41598-018-21798-9
PubMed: 29487297
PubMed Central: PMC5829257
Affiliations:
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Godoy</name><affiliation wicri:level="4"><nlm:affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName><orgName type="university">Université de São Paulo</orgName></affiliation></author><author><name sortKey="Pereira, Caroline S" sort="Pereira, Caroline S" uniqKey="Pereira C" first="Caroline S" last="Pereira">Caroline S. 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Nascimento</name><affiliation wicri:level="4"><nlm:affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName><orgName type="university">Université de São Paulo</orgName></affiliation></author><author><name sortKey="Skaf, Munir S" sort="Skaf, Munir S" uniqKey="Skaf M" first="Munir S" last="Skaf">Munir S. Skaf</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Polikarpov, Igor" sort="Polikarpov, Igor" uniqKey="Polikarpov I" first="Igor" last="Polikarpov">Igor Polikarpov</name><affiliation wicri:level="4"><nlm:affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil. ipolikarpov@ifsc.usp.br.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName><orgName type="university">Université de São Paulo</orgName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018</date><idno type="RBID">pubmed:29487297</idno><idno type="pmid">29487297</idno><idno type="doi">10.1038/s41598-018-21798-9</idno><idno type="pmc">PMC5829257</idno><idno type="wicri:Area/Main/Corpus">000123</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000123</idno><idno type="wicri:Area/Main/Curation">000123</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000123</idno><idno type="wicri:Area/Main/Exploration">000123</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members.</title><author><name sortKey="Godoy, Andre S" sort="Godoy, Andre S" uniqKey="Godoy A" first="Andre S" last="Godoy">Andre S. Godoy</name><affiliation wicri:level="4"><nlm:affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName><orgName type="university">Université de São Paulo</orgName></affiliation></author><author><name sortKey="Pereira, Caroline S" sort="Pereira, Caroline S" uniqKey="Pereira C" first="Caroline S" last="Pereira">Caroline S. Pereira</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Ramia, Marina Paglione" sort="Ramia, Marina Paglione" uniqKey="Ramia M" first="Marina Paglione" last="Ramia">Marina Paglione Ramia</name><affiliation wicri:level="4"><nlm:affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName><orgName type="university">Université de São Paulo</orgName></affiliation></author><author><name sortKey="Silveira, Rodrigo L" sort="Silveira, Rodrigo L" uniqKey="Silveira R" first="Rodrigo L" last="Silveira">Rodrigo L. Silveira</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Camilo, Cesar M" sort="Camilo, Cesar M" uniqKey="Camilo C" first="Cesar M" last="Camilo">Cesar M. Camilo</name><affiliation wicri:level="3"><nlm:affiliation>Centro de Tecnologia Canavieira, Fazenda Santo Antonio, PO Box 162, 13400-970, Piracicaba, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Centro de Tecnologia Canavieira, Fazenda Santo Antonio, PO Box 162, 13400-970, Piracicaba, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Kadowaki, Marco A" sort="Kadowaki, Marco A" uniqKey="Kadowaki M" first="Marco A" last="Kadowaki">Marco A. Kadowaki</name><affiliation wicri:level="4"><nlm:affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName><orgName type="university">Université de São Paulo</orgName></affiliation></author><author><name sortKey="Lange, Lene" sort="Lange, Lene" uniqKey="Lange L" first="Lene" last="Lange">Lene Lange</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby</wicri:regionArea><wicri:noRegion>Lyngby</wicri:noRegion></affiliation></author><author><name sortKey="Busk, Peter K" sort="Busk, Peter K" uniqKey="Busk P" first="Peter K" last="Busk">Peter K. Busk</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby, Denmark.</nlm:affiliation><country xml:lang="fr">Danemark</country><wicri:regionArea>Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby</wicri:regionArea><wicri:noRegion>Lyngby</wicri:noRegion></affiliation></author><author><name sortKey="Nascimento, Alessandro S" sort="Nascimento, Alessandro S" uniqKey="Nascimento A" first="Alessandro S" last="Nascimento">Alessandro S. Nascimento</name><affiliation wicri:level="4"><nlm:affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName><orgName type="university">Université de São Paulo</orgName></affiliation></author><author><name sortKey="Skaf, Munir S" sort="Skaf, Munir S" uniqKey="Skaf M" first="Munir S" last="Skaf">Munir S. Skaf</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName></affiliation></author><author><name sortKey="Polikarpov, Igor" sort="Polikarpov, Igor" uniqKey="Polikarpov I" first="Igor" last="Polikarpov">Igor Polikarpov</name><affiliation wicri:level="4"><nlm:affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil. ipolikarpov@ifsc.usp.br.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo</wicri:regionArea><placeName><settlement type="city">São Paulo</settlement><region type="state">État de São Paulo</region></placeName><orgName type="university">Université de São Paulo</orgName></affiliation></author></analytic><series><title level="j">Scientific reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Catalysis (MeSH)</term><term>Cellulase (chemistry)</term><term>Cellulase (metabolism)</term><term>Computational Biology (MeSH)</term><term>Crystallography, X-Ray (MeSH)</term><term>Enzyme Assays (MeSH)</term><term>Molecular Dynamics Simulation (MeSH)</term><term>Phanerochaete (enzymology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Biologie informatique (MeSH)</term><term>Catalyse (MeSH)</term><term>Cellulase (composition chimique)</term><term>Cellulase (métabolisme)</term><term>Cristallographie aux rayons X (MeSH)</term><term>Dosages enzymatiques (MeSH)</term><term>Phanerochaete (enzymologie)</term><term>Simulation de dynamique moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Cellulase</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Cellulase</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Cellulase</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Phanerochaete</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Phanerochaete</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Cellulase</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Catalysis</term><term>Computational Biology</term><term>Crystallography, X-Ray</term><term>Enzyme Assays</term><term>Molecular Dynamics Simulation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biologie informatique</term><term>Catalyse</term><term>Cristallographie aux rayons X</term><term>Dosages enzymatiques</term><term>Simulation de dynamique moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of β-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general architecture, substrate binding and cleavage. Here, we use a combination of X-ray crystallography, bioinformatics, enzymatic assays, molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure, substrate binding and enzymatic specificity of the GH45 subfamily C endoglucanase from Phanerochaete chrysosporium (PcCel45A). We investigated the role played by different residues in the binding of the enzyme to cellulose oligomers of different lengths and examined the structural characteristics and dynamics of PcCel45A that make subfamily C so dissimilar to other members of the GH45 family. Due to the structural similarity shared between PcCel45A and domain I of expansins, comparative analysis of their substrate binding was also carried out. Our bioinformatics sequence analyses revealed that the hydrolysis mechanisms in GH45 subfamily C is not restricted to use of the imidic asparagine as a general base in the "Newton's cradle" catalytic mechanism recently proposed for this subfamily.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29487297</PMID><DateCompleted><Year>2019</Year><Month>09</Month><Day>23</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>23</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2045-2322</ISSN><JournalIssue CitedMedium="Internet"><Volume>8</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>02</Month><Day>27</Day></PubDate></JournalIssue><Title>Scientific reports</Title><ISOAbbreviation>Sci Rep</ISOAbbreviation></Journal><ArticleTitle>Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members.</ArticleTitle><Pagination><MedlinePgn>3678</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41598-018-21798-9</ELocationID><Abstract><AbstractText>The glycoside hydrolase family 45 (GH45) of carbohydrate modifying enzymes is mostly comprised of β-1,4-endoglucanases. Significant diversity between the GH45 members has prompted the division of this family into three subfamilies: A, B and C, which may differ in terms of the mechanism, general architecture, substrate binding and cleavage. Here, we use a combination of X-ray crystallography, bioinformatics, enzymatic assays, molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure, substrate binding and enzymatic specificity of the GH45 subfamily C endoglucanase from Phanerochaete chrysosporium (PcCel45A). We investigated the role played by different residues in the binding of the enzyme to cellulose oligomers of different lengths and examined the structural characteristics and dynamics of PcCel45A that make subfamily C so dissimilar to other members of the GH45 family. Due to the structural similarity shared between PcCel45A and domain I of expansins, comparative analysis of their substrate binding was also carried out. Our bioinformatics sequence analyses revealed that the hydrolysis mechanisms in GH45 subfamily C is not restricted to use of the imidic asparagine as a general base in the "Newton's cradle" catalytic mechanism recently proposed for this subfamily.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Godoy</LastName><ForeName>Andre S</ForeName><Initials>AS</Initials><Identifier Source="ORCID">0000-0002-0613-9164</Identifier><AffiliationInfo><Affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pereira</LastName><ForeName>Caroline S</ForeName><Initials>CS</Initials><AffiliationInfo><Affiliation>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ramia</LastName><ForeName>Marina Paglione</ForeName><Initials>MP</Initials><AffiliationInfo><Affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Silveira</LastName><ForeName>Rodrigo L</ForeName><Initials>RL</Initials><AffiliationInfo><Affiliation>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Camilo</LastName><ForeName>Cesar M</ForeName><Initials>CM</Initials><Identifier Source="ORCID">0000-0002-3025-5050</Identifier><AffiliationInfo><Affiliation>Centro de Tecnologia Canavieira, Fazenda Santo Antonio, PO Box 162, 13400-970, Piracicaba, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kadowaki</LastName><ForeName>Marco A</ForeName><Initials>MA</Initials><AffiliationInfo><Affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lange</LastName><ForeName>Lene</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Busk</LastName><ForeName>Peter K</ForeName><Initials>PK</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads, Building 229, 2800 Kgs, Lyngby, Denmark.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nascimento</LastName><ForeName>Alessandro S</ForeName><Initials>AS</Initials><AffiliationInfo><Affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Skaf</LastName><ForeName>Munir S</ForeName><Initials>MS</Initials><AffiliationInfo><Affiliation>Institute of Chemistry, University of Campinas, Campinas, 13084-862, São Paulo, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Polikarpov</LastName><ForeName>Igor</ForeName><Initials>I</Initials><Identifier Source="ORCID">0000-0001-9496-4174</Identifier><AffiliationInfo><Affiliation>São Carlos Institute of Physics, University of São Paulo, São Carlos 13566-590, São Paulo, Brazil. ipolikarpov@ifsc.usp.br.</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>2018</Year><Month>02</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Sci 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