Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.03 kDa 
• Atom Count: 6100 
• Modelled Residue Count: 746 
• Deposited Residue Count: 765 
• Unique protein chains: 1

1U1H

A. thaliana cobalamine independent methionine synthase

• DOI: 10.2210/pdb1U1H/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-07-15 Released: 2004-09-02 
• Deposition Author(s): Ferrer, J.-L., Ravanel, S., Robert, M., Dumas, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.260 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Literature

Crystal structures of cobalamin-independent methionine synthase complexed with zinc, homocysteine, and methyltetrahydrofolate

Ferrer, J.-L., Ravanel, S., Robert, M., Dumas, R.

(2004) J Biol Chem 279: 44235-44238

• PubMed: 15326182 
• DOI: 10.1074/jbc.C400325200
• Primary Citation of Related Structures:  
  1U1J, 1U1H, 1U22, 1U1U


• PubMed Abstract: 
  

Cobalamin-independent methionine synthase (MetE) catalyzes the synthesis of methionine by a direct transfer of the methyl group of N5-methyltetrahydrofolate (CH3-H2PteGlun) to the sulfur atom of homocysteine (Hcy). We report here the first crystal structure of this metalloenzyme under different forms, free or complexed with the Hcy and folate substrates. The Arabidopsis thaliana MetE (AtMetE) crystals reveal a monomeric structure built by two (betaalpha)8 barrels making a deep groove at their interface. The active site is located at the surface of the C-terminal domain, facing the large interdomain cleft. Inside the active site, His647, Cys649, and Cys733 are involved in zinc coordination, whereas Asp605, Ile437, and Ser439 interact with Hcy. Opposite the zinc/Hcy binding site, a cationic loop (residues 507-529) belonging to the C-terminal domain anchors the first glutamyl residue of CH3-H4PteGlu5. The pterin moiety of CH3-H4PteGlu5 is stacked with Trp567, enabling the N5-methyl group to protrude in the direction of the zinc atom. These data suggest a structural role of the N-terminal domain of AtMetE in the stabilization of loop 507-529 and in the interaction with the poly-glutamate chain of CH3-H4PteGlun. Comparison of AtMetE structures reveals that the addition of Hcy does not lead to a direct coordination of the sulfur atom with zinc but to a reorganization of the zinc binding site with a stronger coordination to Cys649, Cys733, and a water molecule.

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Organizational Affiliation: 

Laboratoire de Cristallogenèse et Cristallographie des Protéines, Institut de Biologie Structurale J.-P. Ebel, 41 rue Jules Horowitz, 38027 Grenoble 1, France. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase	A	765	Arabidopsis thaliana	Mutation(s): 19  Gene Names: CIMS, MS1, At5g17920, MPI7.9 EC: 2.1.1.14
Find proteins for O50008 (Arabidopsis thaliana) Explore O50008  Go to UniProtKB:  O50008

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MET	A	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.260 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.725	α = 90
b = 121.725	β = 90
c = 132.707	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-15 
• Released Date: 2004-09-02 
Deposition Author(s): Ferrer, J.-L., Ravanel, S., Robert, M., Dumas, R.

Revision History  

• Version 1.0: 2004-09-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance