PDBsum entry: 1u1h

Transferase

PDB id: 1u1h

Contents

Protein chain

746 a.a. *

Ligands

SO4 ×4

MET

Metals

_ZN ×2

Waters ×286

* Residue conservation analysis

PDB id:

1u1h

Name:

Transferase

Title:

A. Thaliana cobalamine independent methionine synthase

Structure:

5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase. Chain: a. Synonym: vitamin-b12-independent methionine synthase isozyme, cobalamin-independent methionine synthase isozyme. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: cims. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.55Å R-factor: 0.214 R-free: 0.260

Authors:

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

Key ref:

J.L.Ferrer et al. (2004). Crystal structures of cobalamin-independent methionine synthase complexed with zinc, homocysteine, and methyltetrahydrofolate. J Biol Chem, 279, 44235-44238. PubMed id: 15326182 DOI: 10.1074/jbc.C400325200

Date:

15-Jul-04 Release date: 02-Sep-04

Protein chain

O50008  (METE_ARATH) -  5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase

Seq: 765 a.a.

Struc: 746 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.1.1.14 - 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase.
• Reaction: 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = tetrahydropteroyltri-L-glutamate + L-methionine

5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = tetrahydropteroyltri-L-glutamate + L-methionine (Bound ligand (Het Group name = MET) corresponds exactly)

• Cofactor: Zinc

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: apoplast (9 terms)
• Biological process: microtubule cytoskeleton organization (6 terms)
• Biochemical function: transferase activity (7 terms)

reference

DOI no: 10.1074/jbc.C400325200

J Biol Chem 279:44235-44238 (2004)

PubMed id: 15326182

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

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

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.

Selected figure(s)

Figure 1.
FIG. 1. Structure of the Arabidopsis MetE. a, ribbon diagram of AtMetE in complex with Met and PteGlu[5]. The Met and PteGlu[5] molecules are depicted as sticks and balls. The N-terminal domain is gold, the C-terminal domain is blue, and the zinc atom is green. b, structural alignment with the Hcy domain of MetH (in pink, code 1Q8A in the Protein Data Bank) performed with DALI. Secondary structures are shown only for residues 416-792 for AtMetE. Diagrams were produced with MOLSCRIPT (22) and rendered with POV-RAY (www.povray.org).

Figure 3.
FIG. 3. Charge colored surface of the methyl donor binding site. This figure, showing AtMetE complexed with CH[3]-H[4]PteGlu[5] and Met, was produced with DINO (Visualizing Structural Biology, 2002, www.dino3d.org).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 44235-44238) copyright 2004.

Figures were selected by an automated process.