PDBsum entry 3cbg

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Transferase PDB id
Protein chain
218 a.a. *
Waters ×124
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Functional and structural characterization of a cationdependent o-methyltransferase from the cyanobacterium synechocystis sp. Strain pcc 6803
Structure: O-methyltransferase. Chain: a. Engineered: yes
Source: Synechocystis sp.. Organism_taxid: 1148. Strain: pcc 6803. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.00Å     R-factor:   0.152     R-free:   0.216
Authors: J.G.Kopycki,P.Neumann,M.T.Stubbs
Key ref:
J.G.Kopycki et al. (2008). Functional and Structural Characterization of a Cation-dependent O-Methyltransferase from the Cyanobacterium Synechocystis sp. Strain PCC 6803. J Biol Chem, 283, 20888-20896. PubMed id: 18502765 DOI: 10.1074/jbc.M801943200
22-Feb-08     Release date:   10-Jun-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q55813  (Q55813_SYNY3) -  O-methyltransferase
220 a.a.
218 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     methylation   1 term 
  Biochemical function     transferase activity     4 terms  


DOI no: 10.1074/jbc.M801943200 J Biol Chem 283:20888-20896 (2008)
PubMed id: 18502765  
Functional and Structural Characterization of a Cation-dependent O-Methyltransferase from the Cyanobacterium Synechocystis sp. Strain PCC 6803.
J.G.Kopycki, M.T.Stubbs, W.Brandt, M.Hagemann, A.Porzel, J.Schmidt, W.Schliemann, M.H.Zenk, T.Vogt.
The coding sequence of the cyanobacterium Synechocystis sp. strain PCC 6803 slr0095 gene was cloned and functionally expressed in Escherichia coli. The corresponding enzyme was classified as a cation- and S-adenosyl-l-methionine-dependent O-methyltransferase (SynOMT), consistent with considerable amino acid sequence identities to eukaryotic O-methyltransferases (OMTs). The substrate specificity of SynOMT was similar with those of plant and mammalian CCoAOMT-like proteins accepting a variety of hydroxycinnamic acids and flavonoids as substrates. In contrast to the known mammalian and plant enzymes, which exclusively methylate the meta-hydroxyl position of aromatic di- and trihydroxy systems, Syn-OMT also methylates the para-position of hydroxycinnamic acids like 5-hydroxyferulic and 3,4,5-trihydroxycinnamic acid, resulting in the formation of novel compounds. The x-ray structure of SynOMT indicates that the active site allows for two alternative orientations of the hydroxylated substrates in comparison to the active sites of animal and plant enzymes, consistent with the observed preferred para-methylation and position promiscuity. Lys(3) close to the N terminus of the recombinant protein appears to play a key role in the activity of the enzyme. The possible implications of these results with respect to modifications of precursors of polymers like lignin are discussed.
  Selected figure(s)  
Figure 5.
FIGURE 5. Reaction schemes comparing product formation with 3,4,5-trihydroxycinnamic acid as substrate. A, SynOMT from Synechocystis sp. strain PCC6803 (SynOMT) and B, PFOMT from M. crystallinum. S, substrate 3,4,5-trihydroxycinnamic acid; P1, 3,5-dihydroxy-4-methoxycinnamic acid; P2, sinapic acid; P3, 5-hydroxy-3,4-dimethoxycinnamic acid; P4, 5-hydroxyferulic acid. In the case of SynOMT, P4, the precursor for P2 and P3, could never be detected by HPLC and is therefore illustrated in reduced intensity.
Figure 6.
FIGURE 6. Structureof SynOMT. A, overall structure of the dimer in schematic representation. The (crystallographically related) monomers are shown in yellow and green, with the N-terminal peptides and insertion loops highlighted. Selected residues at the active site, together with the cofactor AdoMet, the products ferulic and isoferulic acid, are shown in stick representation, whereas the magnesium ions are shown as magenta spheres. B, close up of the active site, together with the experimental 2F[o] - F[c] electron density for the para-methylated product isoferulic acid (pink, in a substrate-like binding mode) and the meta-methylated ferulic acid (light green).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 20888-20896) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20628758 B.G.Kim, D.H.Kim, S.H.Sung, D.E.Kim, Y.Chong, and J.H.Ahn (2010).
Two O-methyltransferases from Picea abies: characterization and molecular basis of different reactivity.
  Planta, 232, 837-844.  
19857499 I.Gómez García, C.E.Stevenson, I.Usón, C.L.Freel Meyers, C.T.Walsh, and D.M.Lawson (2010).
The crystal structure of the novobiocin biosynthetic enzyme NovP: the first representative structure for the TylF O-methyltransferase superfamily.
  J Mol Biol, 395, 390-407.
PDB code: 2wk1
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