PoplarV1, Main, Exploration, bibRecord, 003125

Sequence analysis, in silico modeling and docking studies of caffeoyl CoA-O-methyltransferase of Populus trichopora.

Identifieur interne : 003125 ( Main/Exploration ); précédent : 003124; suivant : 003126

Sequence analysis, in silico modeling and docking studies of caffeoyl CoA-O-methyltransferase of Populus trichopora.

Auteurs : Navneet Phogat ; Vaibhav Vindal ; Vikash Kumar ; Krishna K. Inampudi ; Nirmal K. Prasad

Source :

Journal of molecular modeling [ 0948-5023 ] ; 2010.

RBID : pubmed:20169383

Descripteurs français

English descriptors

KwdEn :
- Amino Acid Sequence (MeSH), Amino Acid Substitution (MeSH), Biocatalysis (MeSH), Catalytic Domain (MeSH), Computational Biology (MeSH), Conserved Sequence (MeSH), Hydrogen Bonding (MeSH), Isoenzymes (chemistry), Isoenzymes (metabolism), Methyltransferases (chemistry), Methyltransferases (metabolism), Models, Molecular (MeSH), Molecular Sequence Data (MeSH), Populus (enzymology), Sequence Alignment (MeSH), Sequence Analysis, Protein (MeSH), Sequence Homology, Amino Acid (MeSH), Substrate Specificity (MeSH).
MESH :
- chemical , chemistry : Isoenzymes, Methyltransferases.
- chemical , metabolism : Isoenzymes, Methyltransferases.
- enzymology : Populus.
- Amino Acid Sequence, Amino Acid Substitution, Biocatalysis, Catalytic Domain, Computational Biology, Conserved Sequence, Hydrogen Bonding, Models, Molecular, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, Protein, Sequence Homology, Amino Acid, Substrate Specificity.

Abstract

Caffeoyl coenzyme A-O-methyltransferases (CCoAOMTs) which are characterized under class I plant OMTs, methylates CoA thioesters, with an in vitro kinetic preference for caffeoyl CoA. CCoAOMTs exhibit association with lignin biosynthesis by showing a prime role in the synthesis of guaiacyl lignin and providing the substrates for synthesis of syringyl lignin. The sequence analysis of CCoAOMT from Populus trichopora exhibits 58 nucleotide substitutions, where transitions overcome transversions. Validation of homology models of both CCoAOMT1 and 2 isoforms reveals that 92.4% and 96% residues are falling in the most favorable region respectively in the Ramachandran plot, indicating CCoAOMT2 as the more satisfactory model, and the overall quality factor of both isoforms is 98.174. The structural architecture analysis is showing very good packing of residues similar to protein crystal structures data. The active site residues and substrate-product interactions showed that CCoAOMT2 possesses more affinity toward caffeoyl CoA, feruloyl CoA, 5-hydroxy feruloyl CoA and sinapoyl CoA than CCoAOMT1, therefore it exist in a more active conformation. The affinity of CCoAOMT2 with feruloyl CoA is highest among all the affinities of both CCoAOMT isoforms with their substrates and products. This information has potential implications to understand the mechanism of CCoAOMT related enzymatic reactions in Populus trichopora, however the approach will be applicable in prediction of substrates and engineering 3D structures of other enzymes as well.

DOI: 10.1007/s00894-010-0656-1
PubMed: 20169383

Affiliations:

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Le document en format XML

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<front><div type="abstract" xml:lang="en">Caffeoyl coenzyme A-O-methyltransferases (CCoAOMTs) which are characterized under class I plant OMTs, methylates CoA thioesters, with an in vitro kinetic preference for caffeoyl CoA. CCoAOMTs exhibit association with lignin biosynthesis by showing a prime role in the synthesis of guaiacyl lignin and providing the substrates for synthesis of syringyl lignin. The sequence analysis of CCoAOMT from Populus trichopora exhibits 58 nucleotide substitutions, where transitions overcome transversions. Validation of homology models of both CCoAOMT1 and 2 isoforms reveals that 92.4% and 96% residues are falling in the most favorable region respectively in the Ramachandran plot, indicating CCoAOMT2 as the more satisfactory model, and the overall quality factor of both isoforms is 98.174. The structural architecture analysis is showing very good packing of residues similar to protein crystal structures data. The active site residues and substrate-product interactions showed that CCoAOMT2 possesses more affinity toward caffeoyl CoA, feruloyl CoA, 5-hydroxy feruloyl CoA and sinapoyl CoA than CCoAOMT1, therefore it exist in a more active conformation. The affinity of CCoAOMT2 with feruloyl CoA is highest among all the affinities of both CCoAOMT isoforms with their substrates and products. This information has potential implications to understand the mechanism of CCoAOMT related enzymatic reactions in Populus trichopora, however the approach will be applicable in prediction of substrates and engineering 3D structures of other enzymes as well.</div>
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<Abstract><AbstractText>Caffeoyl coenzyme A-O-methyltransferases (CCoAOMTs) which are characterized under class I plant OMTs, methylates CoA thioesters, with an in vitro kinetic preference for caffeoyl CoA. CCoAOMTs exhibit association with lignin biosynthesis by showing a prime role in the synthesis of guaiacyl lignin and providing the substrates for synthesis of syringyl lignin. The sequence analysis of CCoAOMT from Populus trichopora exhibits 58 nucleotide substitutions, where transitions overcome transversions. Validation of homology models of both CCoAOMT1 and 2 isoforms reveals that 92.4% and 96% residues are falling in the most favorable region respectively in the Ramachandran plot, indicating CCoAOMT2 as the more satisfactory model, and the overall quality factor of both isoforms is 98.174. The structural architecture analysis is showing very good packing of residues similar to protein crystal structures data. The active site residues and substrate-product interactions showed that CCoAOMT2 possesses more affinity toward caffeoyl CoA, feruloyl CoA, 5-hydroxy feruloyl CoA and sinapoyl CoA than CCoAOMT1, therefore it exist in a more active conformation. The affinity of CCoAOMT2 with feruloyl CoA is highest among all the affinities of both CCoAOMT isoforms with their substrates and products. This information has potential implications to understand the mechanism of CCoAOMT related enzymatic reactions in Populus trichopora, however the approach will be applicable in prediction of substrates and engineering 3D structures of other enzymes as well.</AbstractText>
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<tree><noCountry><name sortKey="Inampudi, Krishna K" sort="Inampudi, Krishna K" uniqKey="Inampudi K" first="Krishna K" last="Inampudi">Krishna K. Inampudi</name>
<name sortKey="Kumar, Vikash" sort="Kumar, Vikash" uniqKey="Kumar V" first="Vikash" last="Kumar">Vikash Kumar</name>
<name sortKey="Phogat, Navneet" sort="Phogat, Navneet" uniqKey="Phogat N" first="Navneet" last="Phogat">Navneet Phogat</name>
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Sequence analysis, in silico modeling and docking studies of caffeoyl CoA-O-methyltransferase of Populus trichopora.

Sequence analysis, in silico modeling and docking studies of caffeoyl CoA-O-methyltransferase of Populus trichopora.

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