4QDJ

Crystal structure of magnesium protoporphyrin IX methyltransferase (ChlM) from Synechocystis PCC 6803 with bound SAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the catalytic mechanism of Synechocystis magnesium protoporphyrin IX O-methyltransferase (ChlM).

Chen, X.Wang, X.Feng, J.Chen, Y.Fang, Y.Zhao, S.Zhao, A.Zhang, M.Liu, L.

(2014) J.Biol.Chem. 289: 25690-25698

  • DOI: 10.1074/jbc.M114.584920
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Magnesium protoporphyrin IX O-methyltransferase (ChlM) catalyzes transfer of the methyl group from S-adenosylmethionine to the carboxyl group of the C13 propionate side chain of magnesium protoporphyrin IX. This reaction is the second committed step ...

    Magnesium protoporphyrin IX O-methyltransferase (ChlM) catalyzes transfer of the methyl group from S-adenosylmethionine to the carboxyl group of the C13 propionate side chain of magnesium protoporphyrin IX. This reaction is the second committed step in chlorophyll biosynthesis from protoporphyrin IX. Here we report the crystal structures of ChlM from the cyanobacterium Synechocystis sp. PCC 6803 in complex with S-adenosylmethionine and S-adenosylhomocysteine at resolutions of 1.6 and 1.7 Å, respectively. The structures illustrate the molecular basis for cofactor and substrate binding and suggest that conformational changes of the two "arm" regions may modulate binding and release of substrates/products to and from the active site. Tyr-28 and His-139 were identified to play essential roles for methyl transfer reaction but are not indispensable for cofactor/substrate binding. Based on these structural and functional findings, a catalytic model is proposed.


    Organizational Affiliation

    From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.,the Engineering Research Center for Biomedical Materials, School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China, and.,From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China, liulin@ibcas.ac.cn.,From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China, the University of Chinese Academy of Sciences, Beijing, 100049, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Magnesium-protoporphyrin O-methyltransferase
A
238Synechocystis sp. (strain PCC 6803 / Kazusa)Mutation(s): 0 
Gene Names: chlM
EC: 2.1.1.11
Find proteins for Q55467 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  Q55467
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.319α = 90.00
b = 61.026β = 90.00
c = 68.892γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Database references