Structural, biochemical, and computational characterization of the glycoside hydrolase family 7 cellobiohydrolase of the tree-killing fungus Heterobasidion irregulare.
Identifieur interne : 000360 ( Main/Exploration ); précédent : 000359; suivant : 000361Structural, biochemical, and computational characterization of the glycoside hydrolase family 7 cellobiohydrolase of the tree-killing fungus Heterobasidion irregulare.
Auteurs : Majid Haddad Momeni [Suède] ; Christina M. Payne ; Henrik Hansson ; Nils Egil Mikkelsen ; Jesper Svedberg ; Ke Engström ; Mats Sandgren ; Gregg T. Beckham ; Jerry St HlbergSource :
- The Journal of biological chemistry [ 1083-351X ] ; 2013.
Descripteurs français
- KwdFr :
- Arbres (microbiologie), Biocarburants (MeSH), Cellulase (composition chimique), Cellulase (métabolisme), Cellulose (métabolisme), Cellulose 1,4-beta-cellobiosidase (métabolisme), Concentration en ions d'hydrogène (MeSH), Conformation moléculaire (MeSH), Cristallographie aux rayons X (méthodes), Données de séquences moléculaires (MeSH), Glycosidases (composition chimique), Glycosidases (métabolisme), Glycosidases (physiologie), Hydrolyse (MeSH), Hypocrea (métabolisme), Ligands (MeSH), Phanerochaete (métabolisme), Similitude de séquences d'acides aminés (MeSH), Simulation numérique (MeSH), Sites de fixation (MeSH), Séquence d'acides aminés (MeSH), Trichoderma (métabolisme).
- MESH :
- composition chimique : Cellulase, Glycosidases.
- microbiologie : Arbres.
- métabolisme : Cellulase, Cellulose, Cellulose 1,4-beta-cellobiosidase, Glycosidases, Hypocrea, Phanerochaete, Trichoderma.
- méthodes : Cristallographie aux rayons X.
- physiologie : Glycosidases.
- Biocarburants, Concentration en ions d'hydrogène, Conformation moléculaire, Données de séquences moléculaires, Hydrolyse, Ligands, Similitude de séquences d'acides aminés, Simulation numérique, Sites de fixation, Séquence d'acides aminés.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Binding Sites (MeSH), Biofuels (MeSH), Cellulase (chemistry), Cellulase (metabolism), Cellulose (metabolism), Cellulose 1,4-beta-Cellobiosidase (metabolism), Computer Simulation (MeSH), Crystallography, X-Ray (methods), Glycoside Hydrolases (chemistry), Glycoside Hydrolases (metabolism), Glycoside Hydrolases (physiology), Hydrogen-Ion Concentration (MeSH), Hydrolysis (MeSH), Hypocrea (metabolism), Ligands (MeSH), Molecular Conformation (MeSH), Molecular Sequence Data (MeSH), Phanerochaete (metabolism), Sequence Homology, Amino Acid (MeSH), Trees (microbiology), Trichoderma (metabolism).
- MESH :
- chemical , chemistry : Cellulase, Glycoside Hydrolases.
- chemical , metabolism : Cellulase, Cellulose, Cellulose 1,4-beta-Cellobiosidase, Glycoside Hydrolases.
- chemical , physiology : Glycoside Hydrolases.
- chemical : Biofuels, Ligands.
- metabolism : Hypocrea, Phanerochaete, Trichoderma.
- methods : Crystallography, X-Ray.
- microbiology : Trees.
- Amino Acid Sequence, Binding Sites, Computer Simulation, Hydrogen-Ion Concentration, Hydrolysis, Molecular Conformation, Molecular Sequence Data, Sequence Homology, Amino Acid.
Abstract
Root rot fungi of the Heterobasidion annosum complex are the most damaging pathogens in temperate forests, and the recently sequenced Heterobasidion irregulare genome revealed over 280 carbohydrate-active enzymes. Here, H. irregulare was grown on biomass, and the most abundant protein in the culture filtrate was identified as the only family 7 glycoside hydrolase in the genome, which consists of a single catalytic domain, lacking a linker and carbohydrate-binding module. The enzyme, HirCel7A, was characterized biochemically to determine the optimal conditions for activity. HirCel7A was crystallized and the structure, refined at 1.7 Å resolution, confirms that HirCel7A is a cellobiohydrolase rather than an endoglucanase, with a cellulose-binding tunnel that is more closed than Phanerochaete chrysosporium Cel7D and more open than Hypocrea jecorina Cel7A, suggesting intermediate enzyme properties. Molecular simulations were conducted to ascertain differences in enzyme-ligand interactions, ligand solvation, and loop flexibility between the family 7 glycoside hydrolase cellobiohydrolases from H. irregulare, H. jecorina, and P. chrysosporium. The structural comparisons and simulations suggest significant differences in enzyme-ligand interactions at the tunnel entrance in the -7 to -4 binding sites and suggest that a tyrosine residue at the tunnel entrance of HirCel7A may serve as an additional ligand-binding site. Additionally, the loops over the active site in H. jecorina Cel7A are more closed than loops in the other two enzymes, which has implications for the degree of processivity, endo-initiation, and substrate dissociation. Overall, this study highlights molecular level features important to understanding this biologically and industrially important family of glycoside hydrolases.
DOI: 10.1074/jbc.M112.440891
PubMed: 23303184
PubMed Central: PMC3581431
Affiliations:
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Here, H. irregulare was grown on biomass, and the most abundant protein in the culture filtrate was identified as the only family 7 glycoside hydrolase in the genome, which consists of a single catalytic domain, lacking a linker and carbohydrate-binding module. The enzyme, HirCel7A, was characterized biochemically to determine the optimal conditions for activity. HirCel7A was crystallized and the structure, refined at 1.7 Å resolution, confirms that HirCel7A is a cellobiohydrolase rather than an endoglucanase, with a cellulose-binding tunnel that is more closed than Phanerochaete chrysosporium Cel7D and more open than Hypocrea jecorina Cel7A, suggesting intermediate enzyme properties. Molecular simulations were conducted to ascertain differences in enzyme-ligand interactions, ligand solvation, and loop flexibility between the family 7 glycoside hydrolase cellobiohydrolases from H. irregulare, H. jecorina, and P. chrysosporium. The structural comparisons and simulations suggest significant differences in enzyme-ligand interactions at the tunnel entrance in the -7 to -4 binding sites and suggest that a tyrosine residue at the tunnel entrance of HirCel7A may serve as an additional ligand-binding site. Additionally, the loops over the active site in H. jecorina Cel7A are more closed than loops in the other two enzymes, which has implications for the degree of processivity, endo-initiation, and substrate dissociation. Overall, this study highlights molecular level features important to understanding this biologically and industrially important family of glycoside hydrolases.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23303184</PMID><DateCompleted><Year>2013</Year><Month>04</Month><Day>25</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>288</Volume><Issue>8</Issue><PubDate><Year>2013</Year><Month>Feb</Month><Day>22</Day></PubDate></JournalIssue><Title>The Journal of biological chemistry</Title><ISOAbbreviation>J Biol Chem</ISOAbbreviation></Journal><ArticleTitle>Structural, biochemical, and computational characterization of the glycoside hydrolase family 7 cellobiohydrolase of the tree-killing fungus Heterobasidion irregulare.</ArticleTitle><Pagination><MedlinePgn>5861-72</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1074/jbc.M112.440891</ELocationID><Abstract><AbstractText>Root rot fungi of the Heterobasidion annosum complex are the most damaging pathogens in temperate forests, and the recently sequenced Heterobasidion irregulare genome revealed over 280 carbohydrate-active enzymes. Here, H. irregulare was grown on biomass, and the most abundant protein in the culture filtrate was identified as the only family 7 glycoside hydrolase in the genome, which consists of a single catalytic domain, lacking a linker and carbohydrate-binding module. The enzyme, HirCel7A, was characterized biochemically to determine the optimal conditions for activity. HirCel7A was crystallized and the structure, refined at 1.7 Å resolution, confirms that HirCel7A is a cellobiohydrolase rather than an endoglucanase, with a cellulose-binding tunnel that is more closed than Phanerochaete chrysosporium Cel7D and more open than Hypocrea jecorina Cel7A, suggesting intermediate enzyme properties. Molecular simulations were conducted to ascertain differences in enzyme-ligand interactions, ligand solvation, and loop flexibility between the family 7 glycoside hydrolase cellobiohydrolases from H. irregulare, H. jecorina, and P. chrysosporium. The structural comparisons and simulations suggest significant differences in enzyme-ligand interactions at the tunnel entrance in the -7 to -4 binding sites and suggest that a tyrosine residue at the tunnel entrance of HirCel7A may serve as an additional ligand-binding site. Additionally, the loops over the active site in H. jecorina Cel7A are more closed than loops in the other two enzymes, which has implications for the degree of processivity, endo-initiation, and substrate dissociation. Overall, this study highlights molecular level features important to understanding this biologically and industrially important family of glycoside hydrolases.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Momeni</LastName><ForeName>Majid Haddad</ForeName><Initials>MH</Initials><AffiliationInfo><Affiliation>Department of Molecular Biology, Swedish University of Agricultural Sciences, SE-751 24 Uppsala, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Payne</LastName><ForeName>Christina M</ForeName><Initials>CM</Initials></Author><Author ValidYN="Y"><LastName>Hansson</LastName><ForeName>Henrik</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Mikkelsen</LastName><ForeName>Nils Egil</ForeName><Initials>NE</Initials></Author><Author ValidYN="Y"><LastName>Svedberg</LastName><ForeName>Jesper</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Engström</LastName><ForeName>Åke</ForeName><Initials>Å</Initials></Author><Author ValidYN="Y"><LastName>Sandgren</LastName><ForeName>Mats</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Beckham</LastName><ForeName>Gregg T</ForeName><Initials>GT</Initials></Author><Author ValidYN="Y"><LastName>Ståhlberg</LastName><ForeName>Jerry</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>PDB</DataBankName><AccessionNumberList><AccessionNumber>2XSP</AccessionNumber><AccessionNumber>2YG1</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>01</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Biol Chem</MedlineTA><NlmUniqueID>2985121R</NlmUniqueID><ISSNLinking>0021-9258</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D056804">Biofuels</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D008024">Ligands</NameOfSubstance></Chemical><Chemical><RegistryNumber>9004-34-6</RegistryNumber><NameOfSubstance UI="D002482">Cellulose</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.-</RegistryNumber><NameOfSubstance UI="D006026">Glycoside Hydrolases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.4</RegistryNumber><NameOfSubstance UI="D002480">Cellulase</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.91</RegistryNumber><NameOfSubstance UI="D043366">Cellulose 1,4-beta-Cellobiosidase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056804" MajorTopicYN="N">Biofuels</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002480" MajorTopicYN="N">Cellulase</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002482" MajorTopicYN="N">Cellulose</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D043366" MajorTopicYN="N">Cellulose 1,4-beta-Cellobiosidase</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018360" MajorTopicYN="N">Crystallography, X-Ray</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006026" MajorTopicYN="N">Glycoside Hydrolases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006863" MajorTopicYN="N">Hydrogen-Ion Concentration</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006868" MajorTopicYN="N">Hydrolysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D035901" MajorTopicYN="N">Hypocrea</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008024" MajorTopicYN="N">Ligands</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008968" MajorTopicYN="N">Molecular Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020075" MajorTopicYN="N">Phanerochaete</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017386" MajorTopicYN="N">Sequence Homology, Amino Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014197" MajorTopicYN="N">Trees</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014242" MajorTopicYN="N">Trichoderma</DescriptorName><QualifierName UI="Q000378" 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