Structural basis for the action of xyloglucan endotransglycosylases/hydrolases: insights from homology modeling.
Identifieur interne : 003106 ( Main/Exploration ); précédent : 003105; suivant : 003107Structural basis for the action of xyloglucan endotransglycosylases/hydrolases: insights from homology modeling.
Auteurs : Qin Xu [États-Unis] ; Xia Ye ; Li-Yan Li ; Zong-Ming Cheng ; Hong GuoSource :
- Interdisciplinary sciences, computational life sciences [ 1913-2751 ] ; 2010.
Descripteurs français
- KwdFr :
- Algorithmes (MeSH), Arabidopsis (enzymologie), Biologie informatique (méthodes), Conformation des protéines (MeSH), Données de séquences moléculaires (MeSH), Glycosyltransferase (composition chimique), Génome végétal (MeSH), Hydrolases (composition chimique), Modèles moléculaires (MeSH), Paroi cellulaire (enzymologie), Populus (enzymologie), Protéines végétales (composition chimique), Protéines végétales (métabolisme), Similitude de séquences d'acides aminés (MeSH), Séquence d'acides aminés (MeSH).
- MESH :
- composition chimique : Glycosyltransferase, Hydrolases, Protéines végétales.
- enzymologie : Arabidopsis, Paroi cellulaire, Populus.
- métabolisme : Protéines végétales.
- méthodes : Biologie informatique.
- Algorithmes, Conformation des protéines, Données de séquences moléculaires, Génome végétal, Modèles moléculaires, Similitude de séquences d'acides aminés, Séquence d'acides aminés.
English descriptors
- KwdEn :
- Algorithms (MeSH), Amino Acid Sequence (MeSH), Arabidopsis (enzymology), Cell Wall (enzymology), Computational Biology (methods), Genome, Plant (MeSH), Glycosyltransferases (chemistry), Hydrolases (chemistry), Models, Molecular (MeSH), Molecular Sequence Data (MeSH), Plant Proteins (chemistry), Plant Proteins (metabolism), Populus (enzymology), Protein Conformation (MeSH), Sequence Homology, Amino Acid (MeSH).
- MESH :
- chemical , chemistry : Glycosyltransferases, Hydrolases, Plant Proteins.
- enzymology : Arabidopsis, Cell Wall, Populus.
- chemical , metabolism : Plant Proteins.
- methods : Computational Biology.
- Algorithms, Amino Acid Sequence, Genome, Plant, Models, Molecular, Molecular Sequence Data, Protein Conformation, Sequence Homology, Amino Acid.
Abstract
Xyloglucan endotransglycosylase/hydrolases (XTH) are believed to play an important role in modifying the cell wall structure through two different, but related actions: the cleavage of a cross-linking xyloglucan polymer (xyloglucan endohydrolase (XEH) activity) and transfer of a newly generated end to another sugar polymer (xyloglucan endotransglycosylase (XET) activity). These enzymes normally show predominantly either XET or XEH. Question remains concerning the origin of the XET or XEH activity of poplar (Populus trichocarpa) XTH proteins as well as the 3-dimensional structural features that might contribute to the different activities for different phylogenetic groups. Previous investigations have demonstrated that the key structural features controlling the activity may involve the loop 1 and 2 regions of the XTH enzymes. Here we report homology models for 40 poplar (Populus trichocarpa) XTH proteins and analyze their loop 1 and 2 regions. These analyses allow us to generate some hypotheses concerning the possible activities of these enzymes. The results show that the protein models for subfamilies (SFs) I/II/IV match well with that of the known XET enzyme (Ptt-XET16-34 from a Populus hybrid), suggesting that they might mainly function as the XET. It is found that the SF III-A models match well with that of the known XEH TmXTH1. Therefore, they may function as XEH as well. Although the SF III-B members are found to have a truncated loop 2, comparison of the homology models with the existing TmXTH1 structure seems to suggest that they might have relatively high possibility to function as XEH instead of XET.
DOI: 10.1007/s12539-010-0070-5
PubMed: 20640780
Affiliations:
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Guo</name></author></analytic><series><title level="j">Interdisciplinary sciences, computational life sciences</title><idno type="ISSN">1913-2751</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms (MeSH)</term><term>Amino Acid Sequence (MeSH)</term><term>Arabidopsis (enzymology)</term><term>Cell Wall (enzymology)</term><term>Computational Biology (methods)</term><term>Genome, Plant (MeSH)</term><term>Glycosyltransferases (chemistry)</term><term>Hydrolases (chemistry)</term><term>Models, Molecular (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Plant Proteins (chemistry)</term><term>Plant Proteins (metabolism)</term><term>Populus (enzymology)</term><term>Protein Conformation (MeSH)</term><term>Sequence Homology, Amino Acid (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes (MeSH)</term><term>Arabidopsis (enzymologie)</term><term>Biologie informatique (méthodes)</term><term>Conformation des protéines (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Glycosyltransferase (composition chimique)</term><term>Génome végétal (MeSH)</term><term>Hydrolases (composition chimique)</term><term>Modèles moléculaires (MeSH)</term><term>Paroi cellulaire (enzymologie)</term><term>Populus (enzymologie)</term><term>Protéines végétales (composition chimique)</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>Glycosyltransferases</term><term>Hydrolases</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Glycosyltransferase</term><term>Hydrolases</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Arabidopsis</term><term>Paroi cellulaire</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Arabidopsis</term><term>Cell Wall</term><term>Populus</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Genome, Plant</term><term>Models, Molecular</term><term>Molecular Sequence Data</term><term>Protein Conformation</term><term>Sequence Homology, Amino Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Conformation des protéines</term><term>Données de séquences moléculaires</term><term>Génome végétal</term><term>Modèles moléculaires</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">Xyloglucan endotransglycosylase/hydrolases (XTH) are believed to play an important role in modifying the cell wall structure through two different, but related actions: the cleavage of a cross-linking xyloglucan polymer (xyloglucan endohydrolase (XEH) activity) and transfer of a newly generated end to another sugar polymer (xyloglucan endotransglycosylase (XET) activity). These enzymes normally show predominantly either XET or XEH. Question remains concerning the origin of the XET or XEH activity of poplar (Populus trichocarpa) XTH proteins as well as the 3-dimensional structural features that might contribute to the different activities for different phylogenetic groups. Previous investigations have demonstrated that the key structural features controlling the activity may involve the loop 1 and 2 regions of the XTH enzymes. Here we report homology models for 40 poplar (Populus trichocarpa) XTH proteins and analyze their loop 1 and 2 regions. These analyses allow us to generate some hypotheses concerning the possible activities of these enzymes. The results show that the protein models for subfamilies (SFs) I/II/IV match well with that of the known XET enzyme (Ptt-XET16-34 from a Populus hybrid), suggesting that they might mainly function as the XET. It is found that the SF III-A models match well with that of the known XEH TmXTH1. Therefore, they may function as XEH as well. Although the SF III-B members are found to have a truncated loop 2, comparison of the homology models with the existing TmXTH1 structure seems to suggest that they might have relatively high possibility to function as XEH instead of XET.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20640780</PMID><DateCompleted><Year>2010</Year><Month>09</Month><Day>21</Day></DateCompleted><DateRevised><Year>2016</Year><Month>05</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1913-2751</ISSN><JournalIssue CitedMedium="Print"><Volume>2</Volume><Issue>2</Issue><PubDate><Year>2010</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Interdisciplinary sciences, computational life sciences</Title><ISOAbbreviation>Interdiscip Sci</ISOAbbreviation></Journal><ArticleTitle>Structural basis for the action of xyloglucan endotransglycosylases/hydrolases: insights from homology modeling.</ArticleTitle><Pagination><MedlinePgn>133-9</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s12539-010-0070-5</ELocationID><Abstract><AbstractText>Xyloglucan endotransglycosylase/hydrolases (XTH) are believed to play an important role in modifying the cell wall structure through two different, but related actions: the cleavage of a cross-linking xyloglucan polymer (xyloglucan endohydrolase (XEH) activity) and transfer of a newly generated end to another sugar polymer (xyloglucan endotransglycosylase (XET) activity). These enzymes normally show predominantly either XET or XEH. Question remains concerning the origin of the XET or XEH activity of poplar (Populus trichocarpa) XTH proteins as well as the 3-dimensional structural features that might contribute to the different activities for different phylogenetic groups. Previous investigations have demonstrated that the key structural features controlling the activity may involve the loop 1 and 2 regions of the XTH enzymes. Here we report homology models for 40 poplar (Populus trichocarpa) XTH proteins and analyze their loop 1 and 2 regions. These analyses allow us to generate some hypotheses concerning the possible activities of these enzymes. The results show that the protein models for subfamilies (SFs) I/II/IV match well with that of the known XET enzyme (Ptt-XET16-34 from a Populus hybrid), suggesting that they might mainly function as the XET. It is found that the SF III-A models match well with that of the known XEH TmXTH1. Therefore, they may function as XEH as well. Although the SF III-B members are found to have a truncated loop 2, comparison of the homology models with the existing TmXTH1 structure seems to suggest that they might have relatively high possibility to function as XEH instead of XET.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Qin</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Xia</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Li-Yan</ForeName><Initials>LY</Initials></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Zong-Ming</ForeName><Initials>ZM</Initials></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Hong</ForeName><Initials>H</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2010</Year><Month>05</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Interdiscip Sci</MedlineTA><NlmUniqueID>101515919</NlmUniqueID><ISSNLinking>1867-1462</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.4.-</RegistryNumber><NameOfSubstance UI="D016695">Glycosyltransferases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.4.1.-</RegistryNumber><NameOfSubstance UI="C073693">xyloglucan 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UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016695" MajorTopicYN="N">Glycosyltransferases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006867" MajorTopicYN="N">Hydrolases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="N">enzymology</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></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2009</Year><Month>08</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2010</Year><Month>03</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2010</Year><Month>03</Month><Day>01</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2010</Year><Month>7</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2010</Year><Month>7</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2010</Year><Month>9</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">20640780</ArticleId><ArticleId IdType="doi">10.1007/s12539-010-0070-5</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Tennessee</li></region></list><tree><noCountry><name sortKey="Cheng, Zong Ming" sort="Cheng, Zong Ming" uniqKey="Cheng Z" first="Zong-Ming" last="Cheng">Zong-Ming Cheng</name><name sortKey="Guo, Hong" sort="Guo, Hong" uniqKey="Guo H" first="Hong" last="Guo">Hong Guo</name><name sortKey="Li, Li Yan" sort="Li, Li Yan" uniqKey="Li L" first="Li-Yan" last="Li">Li-Yan Li</name><name sortKey="Ye, Xia" sort="Ye, Xia" uniqKey="Ye X" first="Xia" last="Ye">Xia Ye</name></noCountry><country name="États-Unis"><region name="Tennessee"><name sortKey="Xu, Qin" sort="Xu, Qin" uniqKey="Xu Q" first="Qin" 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