Journal of Molecular Modeling

, Volume 16, Issue 9, pp 1461–1471

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

  • Navneet Phogat
  • Vaibhav Vindal
  • Vikash Kumar
  • Krishna K. Inampudi
  • Nirmal K. Prasad
Original Paper

DOI: 10.1007/s00894-010-0656-1

Cite this article as:
Phogat, N., Vindal, V., Kumar, V. et al. J Mol Model (2010) 16: 1461. doi:10.1007/s00894-010-0656-1

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.

Keywords

CCoAOMT isoforms Docking Homology modeling Lignin Populus trichopora Sequence analysis 

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Navneet Phogat
    • 1
  • Vaibhav Vindal
    • 2
  • Vikash Kumar
    • 1
  • Krishna K. Inampudi
    • 3
  • Nirmal K. Prasad
    • 1
  1. 1.Department of BiotechnologyGoa UniversityTaleigao PlateauIndia403206
  2. 2.Department of BiotechnologyUniversity of HyderabadGachibowli500046India
  3. 3.Division of Allergy and Infectious Disease, UW medical schoolUniversity of WashingtonSeattleUSA

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