Crystal structures of a Populus tomentosa 4-coumarate:CoA ligase shed light on its enzymatic mechanisms.
Identifieur interne : 003317 ( Main/Exploration ); précédent : 003316; suivant : 003318Crystal structures of a Populus tomentosa 4-coumarate:CoA ligase shed light on its enzymatic mechanisms.
Auteurs : Yonglin Hu [République populaire de Chine] ; Ying Gai ; Lei Yin ; Xiaoxue Wang ; Chunyan Feng ; Lei Feng ; Defeng Li ; Xiang-Ning Jiang ; Da-Cheng WangSource :
- The Plant cell [ 1532-298X ] ; 2010.
Descripteurs français
- KwdFr :
- Alignement de séquences (MeSH), Coenzyme A ligases (composition chimique), Données de séquences moléculaires (MeSH), Mutagenèse dirigée (MeSH), Populus (enzymologie), Protéines végétales (composition chimique), Sites de fixation (MeSH), Spécificité du substrat (MeSH), Structure tertiaire des protéines (MeSH), Séquence d'acides aminés (MeSH).
- MESH :
- composition chimique : Coenzyme A ligases, Protéines végétales.
- enzymologie : Populus.
- Alignement de séquences, Données de séquences moléculaires, Mutagenèse dirigée, Sites de fixation, Spécificité du substrat, Structure tertiaire des protéines, Séquence d'acides aminés.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Coenzyme A Ligases, Plant Proteins.
- enzymology : Populus.
- Amino Acid Sequence, Binding Sites, Molecular Sequence Data, Mutagenesis, Site-Directed, Protein Structure, Tertiary, Sequence Alignment, Substrate Specificity.
Abstract
4-Coumaric acid:CoA ligase (4CL) is the central enzyme of the plant-specific phenylpropanoid pathway. It catalyzes the synthesis of hydroxycinnamate-CoA thioesters, the precursors of lignin and other important phenylpropanoids, in two-step reactions involving the formation of hydroxycinnamate-AMP anhydride and then the nucleophilic substitution of AMP by CoA. In this study, we determined the crystal structures of Populus tomentosa 4CL1 in the unmodified (apo) form and in forms complexed with AMP and adenosine 5'-(3-(4-hydroxyphenyl)propyl)phosphate (APP), an intermediate analog, at 2.4, 2.5, and 1.9 Å resolution, respectively. 4CL1 consists of two globular domains connected by a flexible linker region. The larger N-domain contains a substrate binding pocket, while the C-domain contains catalytic residues. Upon binding of APP, the C-domain rotates 81° relative to the N-domain. The crystal structure of 4CL1-APP reveals its substrate binding pocket. We identified residues essential for catalytic activities (Lys-438, Gln-443, and Lys-523) and substrate binding (Tyr-236, Gly-306, Gly-331, Pro-337, and Val-338) based on their crystal structures and by means of mutagenesis and enzymatic activity studies. We also demonstrated that the size of the binding pocket is the most important factor in determining the substrate specificities of 4CL1. These findings shed light on the enzymatic mechanisms of 4CLs and provide a solid foundation for the bioengineering of these enzymes.
DOI: 10.1105/tpc.109.072652
PubMed: 20841425
PubMed Central: PMC2965553
Affiliations:
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Defeng" sort="Li, Defeng" uniqKey="Li D" first="Defeng" last="Li">Defeng Li</name></author><author><name sortKey="Jiang, Xiang Ning" sort="Jiang, Xiang Ning" uniqKey="Jiang X" first="Xiang-Ning" last="Jiang">Xiang-Ning Jiang</name></author><author><name sortKey="Wang, Da Cheng" sort="Wang, Da Cheng" uniqKey="Wang D" first="Da-Cheng" last="Wang">Da-Cheng Wang</name></author></analytic><series><title level="j">The Plant cell</title><idno type="eISSN">1532-298X</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term><term>Binding Sites (MeSH)</term><term>Coenzyme A Ligases (chemistry)</term><term>Molecular Sequence Data (MeSH)</term><term>Mutagenesis, Site-Directed (MeSH)</term><term>Plant Proteins (chemistry)</term><term>Populus (enzymology)</term><term>Protein Structure, Tertiary (MeSH)</term><term>Sequence Alignment (MeSH)</term><term>Substrate Specificity (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term><term>Coenzyme A ligases (composition chimique)</term><term>Données de séquences moléculaires (MeSH)</term><term>Mutagenèse dirigée (MeSH)</term><term>Populus (enzymologie)</term><term>Protéines végétales (composition chimique)</term><term>Sites de fixation (MeSH)</term><term>Spécificité du substrat (MeSH)</term><term>Structure tertiaire des protéines (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Coenzyme A Ligases</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Coenzyme A ligases</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Binding Sites</term><term>Molecular Sequence Data</term><term>Mutagenesis, Site-Directed</term><term>Protein Structure, Tertiary</term><term>Sequence Alignment</term><term>Substrate Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Données de séquences moléculaires</term><term>Mutagenèse dirigée</term><term>Sites de fixation</term><term>Spécificité du substrat</term><term>Structure tertiaire des protéines</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">4-Coumaric acid:CoA ligase (4CL) is the central enzyme of the plant-specific phenylpropanoid pathway. It catalyzes the synthesis of hydroxycinnamate-CoA thioesters, the precursors of lignin and other important phenylpropanoids, in two-step reactions involving the formation of hydroxycinnamate-AMP anhydride and then the nucleophilic substitution of AMP by CoA. In this study, we determined the crystal structures of Populus tomentosa 4CL1 in the unmodified (apo) form and in forms complexed with AMP and adenosine 5'-(3-(4-hydroxyphenyl)propyl)phosphate (APP), an intermediate analog, at 2.4, 2.5, and 1.9 Å resolution, respectively. 4CL1 consists of two globular domains connected by a flexible linker region. The larger N-domain contains a substrate binding pocket, while the C-domain contains catalytic residues. Upon binding of APP, the C-domain rotates 81° relative to the N-domain. The crystal structure of 4CL1-APP reveals its substrate binding pocket. We identified residues essential for catalytic activities (Lys-438, Gln-443, and Lys-523) and substrate binding (Tyr-236, Gly-306, Gly-331, Pro-337, and Val-338) based on their crystal structures and by means of mutagenesis and enzymatic activity studies. We also demonstrated that the size of the binding pocket is the most important factor in determining the substrate specificities of 4CL1. These findings shed light on the enzymatic mechanisms of 4CLs and provide a solid foundation for the bioengineering of these enzymes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20841425</PMID><DateCompleted><Year>2011</Year><Month>02</Month><Day>07</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1532-298X</ISSN><JournalIssue CitedMedium="Internet"><Volume>22</Volume><Issue>9</Issue><PubDate><Year>2010</Year><Month>Sep</Month></PubDate></JournalIssue><Title>The Plant cell</Title><ISOAbbreviation>Plant Cell</ISOAbbreviation></Journal><ArticleTitle>Crystal structures of a Populus tomentosa 4-coumarate:CoA ligase shed light on its enzymatic mechanisms.</ArticleTitle><Pagination><MedlinePgn>3093-104</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1105/tpc.109.072652</ELocationID><Abstract><AbstractText>4-Coumaric acid:CoA ligase (4CL) is the central enzyme of the plant-specific phenylpropanoid pathway. It catalyzes the synthesis of hydroxycinnamate-CoA thioesters, the precursors of lignin and other important phenylpropanoids, in two-step reactions involving the formation of hydroxycinnamate-AMP anhydride and then the nucleophilic substitution of AMP by CoA. In this study, we determined the crystal structures of Populus tomentosa 4CL1 in the unmodified (apo) form and in forms complexed with AMP and adenosine 5'-(3-(4-hydroxyphenyl)propyl)phosphate (APP), an intermediate analog, at 2.4, 2.5, and 1.9 Å resolution, respectively. 4CL1 consists of two globular domains connected by a flexible linker region. The larger N-domain contains a substrate binding pocket, while the C-domain contains catalytic residues. Upon binding of APP, the C-domain rotates 81° relative to the N-domain. The crystal structure of 4CL1-APP reveals its substrate binding pocket. We identified residues essential for catalytic activities (Lys-438, Gln-443, and Lys-523) and substrate binding (Tyr-236, Gly-306, Gly-331, Pro-337, and Val-338) based on their crystal structures and by means of mutagenesis and enzymatic activity studies. We also demonstrated that the size of the binding pocket is the most important factor in determining the substrate specificities of 4CL1. These findings shed light on the enzymatic mechanisms of 4CLs and provide a solid foundation for the bioengineering of these enzymes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Yonglin</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>National Lab of Biomacromoleucles, Center for Structural and Molecular Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gai</LastName><ForeName>Ying</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Yin</LastName><ForeName>Lei</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xiaoxue</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Chunyan</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Lei</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Defeng</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Xiang-Ning</ForeName><Initials>XN</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Da-Cheng</ForeName><Initials>DC</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GENBANK</DataBankName><AccessionNumberList><AccessionNumber>AY043495</AccessionNumber></AccessionNumberList></DataBank><DataBank><DataBankName>PDB</DataBankName><AccessionNumberList><AccessionNumber>3A9U</AccessionNumber><AccessionNumber>3A9V</AccessionNumber><AccessionNumber>3EQ6</AccessionNumber><AccessionNumber>3NI2</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType 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first="Chunyan" last="Feng">Chunyan Feng</name><name sortKey="Feng, Lei" sort="Feng, Lei" uniqKey="Feng L" first="Lei" last="Feng">Lei Feng</name><name sortKey="Gai, Ying" sort="Gai, Ying" uniqKey="Gai Y" first="Ying" last="Gai">Ying Gai</name><name sortKey="Jiang, Xiang Ning" sort="Jiang, Xiang Ning" uniqKey="Jiang X" first="Xiang-Ning" last="Jiang">Xiang-Ning Jiang</name><name sortKey="Li, Defeng" sort="Li, Defeng" uniqKey="Li D" first="Defeng" last="Li">Defeng Li</name><name sortKey="Wang, Da Cheng" sort="Wang, Da Cheng" uniqKey="Wang D" first="Da-Cheng" last="Wang">Da-Cheng Wang</name><name sortKey="Wang, Xiaoxue" sort="Wang, Xiaoxue" uniqKey="Wang X" first="Xiaoxue" last="Wang">Xiaoxue Wang</name><name sortKey="Yin, Lei" sort="Yin, Lei" uniqKey="Yin L" first="Lei" last="Yin">Lei Yin</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Hu, Yonglin" sort="Hu, Yonglin" uniqKey="Hu Y" first="Yonglin" last="Hu">Yonglin Hu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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{{Explor lien
|wiki= Bois
|area= PoplarV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:20841425
|texte= Crystal structures of a Populus tomentosa 4-coumarate:CoA ligase shed light on its enzymatic mechanisms.
}}
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