PhanerochaeteV1, Main, Exploration, bibRecord, 000478

Understanding lignin-degrading reactions of ligninolytic enzymes: binding affinity and interactional profile.

Identifieur interne : 000478 ( Main/Exploration ); précédent : 000477; suivant : 000479

Understanding lignin-degrading reactions of ligninolytic enzymes: binding affinity and interactional profile.

Auteurs : Ming Chen [République populaire de Chine] ; Guangming Zeng ; Zhongyang Tan ; Min Jiang ; Hui Li ; Lifeng Liu ; Yi Zhu ; Zhen Yu ; Zhen Wei ; Yuanyuan Liu ; Gengxin Xie

Source :

PloS one [ 1932-6203 ] ; 2011.

RBID : pubmed:21980516

Descripteurs français

KwdFr :
- Conformation des protéines (MeSH), Laccase (composition chimique), Laccase (métabolisme), Liaison aux protéines (MeSH), Lignine (métabolisme), Oxidoreductases (composition chimique), Oxidoreductases (métabolisme), Peroxidases (composition chimique), Peroxidases (métabolisme), Phanerochaete (enzymologie), Simulation de dynamique moléculaire (MeSH), Trametes (enzymologie).
MESH :
- composition chimique : Laccase, Oxidoreductases, Peroxidases.
- enzymologie : Phanerochaete, Trametes.
- métabolisme : Laccase, Lignine, Oxidoreductases, Peroxidases.
- Conformation des protéines, Liaison aux protéines, Simulation de dynamique moléculaire.

English descriptors

KwdEn :
- Laccase (chemistry), Laccase (metabolism), Lignin (metabolism), Molecular Dynamics Simulation (MeSH), Oxidoreductases (chemistry), Oxidoreductases (metabolism), Peroxidases (chemistry), Peroxidases (metabolism), Phanerochaete (enzymology), Protein Binding (MeSH), Protein Conformation (MeSH), Trametes (enzymology).
MESH :
- chemical , chemistry : Laccase, Oxidoreductases, Peroxidases.
- chemical , metabolism : Laccase, Lignin, Oxidoreductases, Peroxidases.
- enzymology : Phanerochaete, Trametes.
- Molecular Dynamics Simulation, Protein Binding, Protein Conformation.

Abstract

Previous works have demonstrated that ligninolytic enzymes mediated effective degradation of lignin wastes. The degrading ability greatly relied on the interactions of ligninolytic enzymes with lignin. Ligninolytic enzymes mainly contain laccase (Lac), lignin peroxidase (LiP) and manganese peroxidase (MnP). In the present study, the binding modes of lignin to Lac, LiP and MnP were systematically determined, respectively. Robustness of these modes was further verified by molecular dynamics (MD) simulations. Residues GLU460, PRO346 and SER113 in Lac, residues ARG43, ALA180 and ASP183 in LiP and residues ARG42, HIS173 and ARG177 in MnP were most crucial in binding of lignin, respectively. Interactional analyses showed hydrophobic contacts were most abundant, playing an important role in the determination of substrate specificity. This information is an important contribution to the details of enzyme-catalyzed reactions in the process of lignin biodegradation, which can be used as references for designing enzyme mutants with a better lignin-degrading activity.

DOI: 10.1371/journal.pone.0025647
PubMed: 21980516
PubMed Central: PMC3183068

Affiliations:

République populaire de Chine

Links toward previous steps (curation, corpus...)

to stream Main, to step Corpus: 000474
to stream Main, to step Curation: 000474

Le document en format XML

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<front><div type="abstract" xml:lang="en">Previous works have demonstrated that ligninolytic enzymes mediated effective degradation of lignin wastes. The degrading ability greatly relied on the interactions of ligninolytic enzymes with lignin. Ligninolytic enzymes mainly contain laccase (Lac), lignin peroxidase (LiP) and manganese peroxidase (MnP). In the present study, the binding modes of lignin to Lac, LiP and MnP were systematically determined, respectively. Robustness of these modes was further verified by molecular dynamics (MD) simulations. Residues GLU460, PRO346 and SER113 in Lac, residues ARG43, ALA180 and ASP183 in LiP and residues ARG42, HIS173 and ARG177 in MnP were most crucial in binding of lignin, respectively. Interactional analyses showed hydrophobic contacts were most abundant, playing an important role in the determination of substrate specificity. This information is an important contribution to the details of enzyme-catalyzed reactions in the process of lignin biodegradation, which can be used as references for designing enzyme mutants with a better lignin-degrading activity.</div>
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<Abstract><AbstractText>Previous works have demonstrated that ligninolytic enzymes mediated effective degradation of lignin wastes. The degrading ability greatly relied on the interactions of ligninolytic enzymes with lignin. Ligninolytic enzymes mainly contain laccase (Lac), lignin peroxidase (LiP) and manganese peroxidase (MnP). In the present study, the binding modes of lignin to Lac, LiP and MnP were systematically determined, respectively. Robustness of these modes was further verified by molecular dynamics (MD) simulations. Residues GLU460, PRO346 and SER113 in Lac, residues ARG43, ALA180 and ASP183 in LiP and residues ARG42, HIS173 and ARG177 in MnP were most crucial in binding of lignin, respectively. Interactional analyses showed hydrophobic contacts were most abundant, playing an important role in the determination of substrate specificity. This information is an important contribution to the details of enzyme-catalyzed reactions in the process of lignin biodegradation, which can be used as references for designing enzyme mutants with a better lignin-degrading activity.</AbstractText>
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<Reference><Citation>J Med Chem. 2003 Jun 5;46(12):2287-303</Citation>
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<Reference><Citation>J Chem Theory Comput. 2008 Mar;4(3):435-47</Citation>
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<name sortKey="Liu, Lifeng" sort="Liu, Lifeng" uniqKey="Liu L" first="Lifeng" last="Liu">Lifeng Liu</name>
<name sortKey="Liu, Yuanyuan" sort="Liu, Yuanyuan" uniqKey="Liu Y" first="Yuanyuan" last="Liu">Yuanyuan Liu</name>
<name sortKey="Tan, Zhongyang" sort="Tan, Zhongyang" uniqKey="Tan Z" first="Zhongyang" last="Tan">Zhongyang Tan</name>
<name sortKey="Wei, Zhen" sort="Wei, Zhen" uniqKey="Wei Z" first="Zhen" last="Wei">Zhen Wei</name>
<name sortKey="Xie, Gengxin" sort="Xie, Gengxin" uniqKey="Xie G" first="Gengxin" last="Xie">Gengxin Xie</name>
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<name sortKey="Zeng, Guangming" sort="Zeng, Guangming" uniqKey="Zeng G" first="Guangming" last="Zeng">Guangming Zeng</name>
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Understanding lignin-degrading reactions of ligninolytic enzymes: binding affinity and interactional profile.

Understanding lignin-degrading reactions of ligninolytic enzymes: binding affinity and interactional profile.

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