Abstract
Caffeoyl coenzyme A O-methyltransferase (CCoAOMT) is an important enzyme that participates in lignin biosynthesis especially in the formation of cell wall ferulic esters of plants. It plays a pivotal role in the methylation of the 3-hydroxyl group of caffeoyl CoA. Two cDNA clones that code CCoAOMT were isolated earlier from subabul and in the present study; 3D models of CCoAOMT1 and CCoAOMT2 enzymes were built using the MODELLER7v7 software to find out the substrate binding sites. These two proteins differed only in two amino acids and may have little or no functional redundancy. Refined models of the proteins were obtained after energy minimization and molecular dynamics in a solvated water layer. The models were further assessed by PROCHECK, WHATCHECK, Verify_3D and ERRAT programs and the results indicated that these models are reliable for further active site and docking analysis. The refined models showed that the two proteins have 9 and 10 α-helices, 6 and 7 β-sheets respectively. The models were used for docking the substrates CoA, SAM, SAH, caffeoyl CoA, feruloyl CoA, 5-hydroxy feruloyl CoA and sinapyl CoA which showed that CoA and caffeoyl CoA are binding with high affinity with the enzymes in the presence and absence of SAM. It appears therefore that caffeoyl CoA is the substrate for both the isoenzymes. The results also indicated that CoA and caffeoyl CoA are binding with higher affinity to CCoAOMT2 than CCoAOMT1. Therefore, CCoAOMT2 conformation is thought to be the active form that exists in subabul. Docking studies indicated that conserved active site residues Met58, Thr60, Val63, Glu82, Gly84, Ser90, Asp160, Asp162, Thr169, Asn191 and Arg203 in CCoAOMT1 and CCoAOMT2 enzymes create the positive charge to balance the negatively charged caffeoyl CoA and play an important role in maintaining a functional conformation and are directly involved in donor-substrate binding.
Similar content being viewed by others
References
Higuchi T (1998) Kung S-D, Yang S-F (eds) Discoveries in plant biology. World Scientific, Singapore, 233–269
Grima-Pettenati J, Goffner D (1999) Plant Sci 145:51–65
Meyer K, Sirley AM, Cusumano JC, Bell D Lelong A, Chappel C (1998) Proc Natl Acad Sci USA 95:6619–6623
Tsai CJ, Mielke MR, Hu WJ, Podila GK, Chiang VL (1998) Plant Physiol 117:101–112
Zhong R, Morrison WH, Negrel J, Ye ZH (1998) Plant Cell 10:2033–2045
Ye ZH, Kneusel RE, Matern U, Varner JE (1994) Plant Cell 6:1427–1439
Ye ZH, Varner JE (1995) Plant Physiol 108:459–467
Ye ZH (1997) Plant Physiol 115:1341–1350
Inoue K, Vincent JH, Sewalt G, Balance MNIW, Sturzer C, Dixon RA (1998) Plant Physiol 117:761–770
Martz F, Maury S, Pincon G, Legrand M (1998) Plant Mol Biol 36:427–437
Kersey R, Inoue K, Schubert KR, Dixon RA (1999) Protoplasma 209:46–57
Li L, Osakabe K, Joshi CP, Chiang VL (1999) Plant Mol Biol 40:555–565
Meng H, Campbell WH (1998) Plant Mol Biol 38:513–520
Maury S, Geoffroy P, Legrand M (1999) Plant Physiol 121:215–224
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DJ (1997) Nucleic Acids Res 24:4876–4882
Nicholas KB, Nicholas HB (1997) http://www.psc.edu/biomed/genedoc [Online.]
Page RDM (1996) Comput Appl Biosci 12:357–358
Perrière G, Gouy M (1996) Biochimie 78:364–369
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) J Mol Biol 215:403–410
Ferrer J, Zubeita C, Dixon RA, Noel JP (2005) Plant Physiol 137:1009–1017
Needleman SB, Wunsch CD (1970) J Mol Biol 48:443–453
Sali A, Blundell TL (1993) J Mol Biol 234:779–815
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck J, Field M, Fischer JS, Gao J, Guo H, Ha S (1998) J Phys Chem B 102:3586–3616
Sali A, Overington JP (1994) Protein Sci 3:1582–1596
Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K (1999) J Comput Phys 151:283
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck J, Field M, Fischer JS, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1992) FASEB J 6:A143–A143
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck J, Field M, Fischer JS, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher IWE, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998a) J Phys Chem B 102:3586–3616
Schlenkrich M, Brickmann J, MacKerell AD Jr, Karplus M (1996) A molecular perspective from computation and experiment. In: Merz KM, Roux B (eds) Birkhauser, Boston MA, pp 31–81
Jorgensen WL, Chandresekhar J, Madura JD, Impey RW, Klein ML (1983) J Chem Phys 79:926–935
Grubmuller H, Heller H, Windemuth A, Schulten K (1991) Mol Sim 6:121–142
Schlick T, Skeel R, Brunger A, Kale L, Board JA Jr, Hermans J, Schulten K (1999) Algorithmic challenges in computational molecular biophysics. J Comput Phys 151:9–48
Brunger (1992) X-PLOR, Version 3.1: Yale University New Haven CT
MacKerell AD Jr, Brooks B, Brooks CL III, Nilsson L, Roux B, Won Y, Karplus M (1998b) In: Schleyer P (ed) The encyclopedia of computational chemistry. John Wiley & Sons, Chichester, UK, pp 271–277
Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) J Comput Phys 23:327–341
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) J Chem Phys 103:8577
Laskoswki RA, MacArthur MW, Moss DS, Thorton JM (1993) J Appl Cryst 26:283–291
Colovos K, Yeates TO (1993) Protein Sci 2:1511–1519
Vriend G (1990) J Mol Graph 8:52–56
Hooft RWW, Vriend G, Sander C, Abola EE (1996) Nature 381:272
Guex N, Peitsch MC (1997) Electrophoresis 18:2714–2723
Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J (2006) Nucleic Acids Res 34:W116–W118
Schulz-Gasch T, Stahl M (2003) J Mol Model 9:47–57
Rossmann MG, Moras D, Olsen KW (1974) Nature 250:194–199
Zhong RW, Morrison H III, Himmelsbach DS, Poole FL II, Ye ZH (2000) Plant Physiol 124:563–577
Hoffmann L, Maury S, Bergdoll M, Thion L, Erard M, Legrand M (2001) J Biol Chem 276:36831–36838
Acknowledgements
The authors are thankful to the CSIR, New Delhi, for financial assistance in the form of a research project (CSIR-NMITLI) on paper and pulp.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Sekhar Pagadala, N., Arha, M., Reddy, P.S. et al. Phylogenetic analysis, homology modelling, molecular dynamics and docking studies of caffeoyl–CoA-O- methyl transferase (CCoAOMT 1 and 2) isoforms isolated from subabul (Leucaena leucocephala). J Mol Model 15, 203–221 (2009). https://doi.org/10.1007/s00894-008-0395-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00894-008-0395-8