1M6E

CRYSTAL STRUCTURE OF SALICYLIC ACID CARBOXYL METHYLTRANSFERASE (SAMT)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural Basis for Substrate Recognition in The Salicylic Acid Carboxyl Methyltransferase Family

Zubieta, C., Ross, J.R., Koscheski, P., Yang, Y., Pichersky, E., Noel, J.P.

(2003) Plant Cell 15: 1704-1716

  • DOI: 10.1105/tpc.014548
  • Primary Citation of Related Structures:  
    1M6E

  • PubMed Abstract: 

    • Recently, a novel family of methyltransferases was identified in plants. Some members of this newly discovered and recently characterized methyltransferase family catalyze the formation of small-molecule methyl esters using S-adenosyl-L-Met (SAM) as a methyl donor and carboxylic acid-bearing substrates as methyl acceptors ...

    Recently, a novel family of methyltransferases was identified in plants. Some members of this newly discovered and recently characterized methyltransferase family catalyze the formation of small-molecule methyl esters using S-adenosyl-L-Met (SAM) as a methyl donor and carboxylic acid-bearing substrates as methyl acceptors. These enzymes include SAMT (SAM:salicylic acid carboxyl methyltransferase), BAMT (SAM:benzoic acid carboxyl methyltransferase), and JMT (SAM:jasmonic acid carboxyl methyltransferase). Moreover, other members of this family of plant methyltransferases have been found to catalyze the N-methylation of caffeine precursors. The 3.0-A crystal structure of Clarkia breweri SAMT in complex with the substrate salicylic acid and the demethylated product S-adenosyl-L-homocysteine reveals a protein structure that possesses a helical active site capping domain and a unique dimerization interface. In addition, the chemical determinants responsible for the selection of salicylic acid demonstrate the structural basis for facile variations of substrate selectivity among functionally characterized plant carboxyl-directed and nitrogen-directed methyltransferases and a growing set of related proteins that have yet to be examined biochemically. Using the three-dimensional structure of SAMT as a guide, we examined the substrate specificity of SAMT by site-directed mutagenesis and activity assays against 12 carboxyl-containing small molecules. Moreover, the utility of structural information for the functional characterization of this large family of plant methyltransferases was demonstrated by the discovery of an Arabidopsis methyltransferase that is specific for the carboxyl-bearing phytohormone indole-3-acetic acid.

    Organizational Affiliation: 

    Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase X359Clarkia breweriMutation(s): 0 
Gene Names: SAMT
EC: 2.1.1.274
Find proteins for Q9SPV4 (Clarkia breweri)
Explore Q9SPV4 
Go to UniProtKB:  Q9SPV4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download Ideal Coordinates CCD File 
X
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
LU
Query on LU
Download Ideal Coordinates CCD File 
X
LUTETIUM (III) ION
Lu
PSDMOPINLDTFSZ-UHFFFAOYSA-N		 Ligand Interaction
SAL
Query on SAL
Download Ideal Coordinates CCD File 
X
2-HYDROXYBENZOIC ACID
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.225 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.74α = 90
b = 141.74β = 90
c = 63.983γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance