3DUW

Crystal Structural Analysis of the O-methyltransferase from Bacillus cereus in complex SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and functional insights into O-methyltransferase from Bacillus cereus

Cho, J.-H.Park, Y.Ahn, J.-H.Lim, Y.Rhee, S.

(2008) J Mol Biol 382: 987-997

  • DOI: 10.1016/j.jmb.2008.07.080
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The specific substrates, mechanisms, and structures of the bacterial O-methyltransferases (OMTs) are not as well characterized as those of other OMTs. Recent studies have suggested that bacterial OMTs catalyze regiospecific reactions that might be us ...

    The specific substrates, mechanisms, and structures of the bacterial O-methyltransferases (OMTs) are not as well characterized as those of other OMTs. Recent studies have suggested that bacterial OMTs catalyze regiospecific reactions that might be used to produce novel compounds. In this study, we investigated the structural and functional features of an OMT from Bacillus cereus (BcOMT2). This enzyme catalyzes the O-methylation of flavonoids in vitro in an S-adenosylmethionine-dependent and regiospecific manner. We solved the crystal structures of the BcOMT2 apoenzyme and the BcOMT2-S-adenosylhomocysteine (SAH) co-complex at resolutions of 1.8 and 1.2 A, respectively. These structures reveal that the overall structure of dimeric BcOMT2 is similar to that of the canonical OMT but that BcOMT2 also has a unique N-terminal helical region that is responsible for dimerization. The binding of SAH causes both local and remote conformational changes in the dimer interface that stabilize the dimerization of BcOMT2. SAH binding also causes ordering of residues Glu171 to Gly186, which are disordered in the apoenzyme structure and are known determinants of substrate specificity, and thus contributes to formation of the substrate binding pocket. Our structural analysis indicated a resemblance between the active site of BcOMT2 and that of metal-dependent OMTs. Using mutational analysis, we confirmed that BcOMT2 is a Mg(2+)-dependent OMT. These results provide structural and functional insights into the dimerization mechanism and substrate specificity of BcOMT2.


    Organizational Affiliation

    Department of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Seoul 151-921, Korea.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-methyltransferase, putative
A, B
223Bacillus cereus ATCC 10987Mutation(s): 0 
Gene Names: BCE_2045
EC: 2.1.1
Find proteins for Q739U3 (Bacillus cereus (strain ATCC 10987 / NRS 248))
Go to UniProtKB:  Q739U3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.6α = 90
b = 74.3β = 90
c = 90.6γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-07-18 
  • Released Date: 2008-08-05 
  • Deposition Author(s): Cho, J.-H., Rhee, S.

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance