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Transferase PDB id
1kyw
Jmol
Contents
Protein chains
350 a.a. *
Ligands
SAH ×2
HFL
Waters ×224
* Residue conservation analysis
PDB id:
1kyw
Name: Transferase
Title: Crystal structure analysis of caffeic acid/5-hydroxyferulic acid 3/5-o-methyltransferase in complex with 5- hydroxyconiferaldehyde
Structure: Caffeic acid 3-o-methyltransferase. Chain: a, c, f. Synonym: comt. Engineered: yes
Source: Medicago sativa. Organism_taxid: 3879. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
Resolution:
2.40Å     R-factor:   0.207     R-free:   0.261
Authors: C.Zubieta,P.Kota,J.-L.Ferrer,R.A.Dixon,J.P.Noel
Key ref: C.Zubieta et al. (2002). Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase. Plant Cell, 14, 1265-1277. PubMed id: 12084826 DOI: 10.1105/tpc.001412
Date:
06-Feb-02     Release date:   28-Aug-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P28002  (COMT1_MEDSA) -  Caffeic acid 3-O-methyltransferase
Seq:
Struc: 		365 a.a.
350 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.68  - Caffeate O-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + 3,4-dihydroxy-trans-cinnamate = S-adenosyl-L- homocysteine + 3-methoxy-4-hydroxy-trans-cinnamate
S-adenosyl-L-methionine
 + 3,4-dihydroxy-trans-cinnamate
 =
S-adenosyl-L- homocysteine
Bound ligand (Het Group name = SAH)
corresponds exactly 		+
3-methoxy-4-hydroxy-trans-cinnamate
Bound ligand (Het Group name = HFL)
matches with 93.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     lignin biosynthetic process   1 term 
  Biochemical function     transferase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1105/tpc.001412 Plant Cell 14:1265-1277 (2002)
PubMed id: 12084826  
 
 
Structural basis for the modulation of lignin monomer methylation by caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase.
C.Zubieta, P.Kota, J.L.Ferrer, R.A.Dixon, J.P.Noel.
 
  ABSTRACT  
 
Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase (COMT) from alfalfa is an S-adenosyl-L-Met-dependent O-methyltransferase involved in lignin biosynthesis. COMT methylates caffeoyl- and 5-hydroxyferuloyl-containing acids, aldehydes, and alcohols in vitro while displaying a kinetic preference for the alcohols and aldehydes over the free acids. The 2.2-A crystal structure of COMT in complex with S-adenosyl-L-homocysteine (SAH) and ferulic acid (ferulate form), as well as the 2.4-A crystal structure of COMT in complex with SAH and 5-hydroxyconiferaldehyde, provide a structural understanding of the observed substrate preferences. These crystal structures identify residues lining the active site surface that contact the substrates. Structurally guided site-directed mutagenesis of active site residues was performed with the goal of altering the kinetic preferences for physiological substrates. The kinetic parameters of the COMT mutants versus wild-type enzyme are presented, and coupled with the high-resolution crystal structures, they will serve as a starting point for the in vivo manipulation of lignin monomers in transgenic plants. Ultimately, this structurally based approach to metabolic engineering will allow the further alteration of the lignin biosynthetic pathway in agronomically important plants. This approach will lead to a better understanding of the in vivo operation of the potential metabolic grid for monolignol biosynthesis.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205206 G.Guirimand, A.Guihur, O.Ginis, P.Poutrain, F.Héricourt, A.Oudin, A.Lanoue, B.St-Pierre, V.Burlat, and V.Courdavault (2011).
The subcellular organization of strictosidine biosynthesis in Catharanthus roseus epidermis highlights several trans-tonoplast translocations of intermediate metabolites.
  FEBS J, 278, 749-763.  
20670441 J.M.Zhou, E.Lee, F.Kanapathy-Sinnaiaha, Y.Park, J.A.Kornblatt, Y.Lim, and R.K.Ibrahim (2010).
Structure-function relationships of wheat flavone O-methyltransferase: Homology modeling and site-directed mutagenesis.
  BMC Plant Biol, 10, 156.  
20352262 M.B.Damaj, S.P.Kumpatla, C.Emani, P.D.Beremand, A.S.Reddy, K.S.Rathore, M.T.Buenrostro-Nava, I.S.Curtis, T.L.Thomas, and T.E.Mirkov (2010).
Sugarcane DIRIGENT and O-methyltransferase promoters confer stem-regulated gene expression in diverse monocots.
  Planta, 231, 1439-1458.  
19875443 M.W.Bhuiya, and C.J.Liu (2010).
Engineering monolignol 4-O-methyltransferases to modulate lignin biosynthesis.
  J Biol Chem, 285, 277-285.  
20169383 N.Phogat, V.Vindal, V.Kumar, K.K.Inampudi, and N.K.Prasad (2010).
Sequence analysis, in silico modeling and docking studies of Caffeoyl CoA-O-methyltransferase of Populus trichopora.
  J Mol Model, 16, 1461-1471.  
20689233 T.Morishige, M.Tamakoshi, T.Takemura, and F.Sato (2010).
Molecular characterization of O-methyltransferases involved in isoquinoline alkaloid biosynthesis in Coptis japonica.
  Proc Jpn Acad Ser B Phys Biol Sci, 86, 757-768.  
17988223 B.Rohde, J.Hans, S.Martens, A.Baumert, P.Hunziker, and U.Matern (2008).
Anthranilate N-methyltransferase, a branch-point enzyme of acridone biosynthesis.
  Plant J, 53, 541-553.  
18413608 G.Scalliet, F.Piola, C.J.Douady, S.Réty, O.Raymond, S.Baudino, K.Bordji, M.Bendahmane, C.Dumas, J.M.Cock, and P.Hugueney (2008).
Scent evolution in Chinese roses.
  Proc Natl Acad Sci U S A, 105, 5927-5932.  
18397325 J.A.Kornblatt, J.M.Zhou, and R.K.Ibrahim (2008).
Structure-activity relationships of wheat flavone O-methyltransferase: a homodimer of convenience.
  FEBS J, 275, 2255-2266.  
18923536 J.H.Jung, M.J.Hong, D.Y.Kim, J.Y.Kim, H.Y.Heo, T.H.Kim, C.S.Jang, and Y.W.Seo (2008).
Structural and expressional divergence of genes encoding O-methyltransferase in wheat.
  Genome, 51, 856-869.  
18502766 S.Singh, J.G.McCoy, C.Zhang, C.A.Bingman, G.N.Phillips, and J.S.Thorson (2008).
Structure and mechanism of the rebeccamycin sugar 4'-O-methyltransferase RebM.
  J Biol Chem, 283, 22628-22636.
PDB code: 3bus
17333502 A.Berim, B.Schneider, and M.Petersen (2007).
Methyl allyl ether formation in plants: novel S-adenosyl L-methionine:coniferyl alcohol 9-O-methyltransferase from suspension cultures of three Linum species.
  Plant Mol Biol, 64, 279-291.  
17426774 B.De Nardi, R.Dreos, L.Del Terra, C.Martellossi, E.Asquini, P.Tornincasa, D.Gasperini, B.Pacchioni, R.Rathinavelu, A.Pallavicini, and G.Graziosi (2006).
Differential responses of Coffea arabica L. leaves and roots to chemically induced systemic acquired resistance.
  Genome, 49, 1594-1605.  
17001495 B.E.Deavours, C.J.Liu, M.A.Naoumkina, Y.Tang, M.A.Farag, L.W.Sumner, J.P.Noel, and R.A.Dixon (2006).
Functional analysis of members of the isoflavone and isoflavanone O-methyltransferase enzyme families from the model legume Medicago truncatula.
  Plant Mol Biol, 62, 715-733.  
16623883 H.Coiner, G.Schröder, E.Wehinger, C.J.Liu, J.P.Noel, W.Schwab, and J.Schröder (2006).
Methylation of sulfhydryl groups: a new function for a family of small molecule plant O-methyltransferases.
  Plant J, 46, 193-205.  
16830185 H.M.Li, D.Rotter, T.G.Hartman, F.E.Pak, D.Havkin-Frenkel, and F.C.Belanger (2006).
Evolution of novel O-methyltransferases from the Vanilla planifolia caffeic acid O-methyltransferase.
  Plant Mol Biol, 61, 537-552.  
  16946471 N.Gohain, L.S.Thomashow, D.V.Mavrodi, and W.Blankenfeldt (2006).
The purification, crystallization and preliminary structural characterization of PhzM, a phenazine-modifying methyltransferase from Pseudomonas aeruginosa.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 887-890.  
16356847 I.Fujii, N.Yoshida, S.Shimomaki, H.Oikawa, and Y.Ebizuka (2005).
An iterative type I polyketide synthase PKSN catalyzes synthesis of the decaketide alternapyrone with regio-specific octa-methylation.
  Chem Biol, 12, 1301-1309.  
15860431 R.A.Dixon (2005).
Engineering of plant natural product pathways.
  Curr Opin Plant Biol, 8, 329-336.  
15930622 X.Ma, J.Koepke, A.Bayer, G.Fritzsch, H.Michel, and J.Stöckigt (2005).
Crystallization and preliminary X-ray analysis of native and selenomethionyl vinorine synthase from Rauvolfia serpentina.
  Acta Crystallogr D Biol Crystallogr, 61, 694-696.  
14769935 B.Hamberger, and K.Hahlbrock (2004).
The 4-coumarate:CoA ligase gene family in Arabidopsis thaliana comprises one rare, sinapate-activating and three commonly occurring isoenzymes.
  Proc Natl Acad Sci U S A, 101, 2209-2214.  
15725058 B.S.Winkel (2004).
Metabolic channeling in plants.
  Annu Rev Plant Biol, 55, 85.  
15499381 J.Kornblatt, I.Muzac, Y.Lim, J.H.Ahn, and R.K.Ibrahim (2004).
Role of Serine 286 in cosubstrate binding and catalysis of a flavonol O-methyltransferase.
  Biochem Cell Biol, 82, 531-537.  
  14624860 J.Gressel, and A.Zilberstein (2003).
Let them eat (GM) straw.
  Trends Biotechnol, 21, 525-530.  
14503002 W.Boerjan, J.Ralph, and M.Baucher (2003).
Lignin biosynthesis.
  Annu Rev Plant Biol, 54, 519-546.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.