PDBsum entry 1f6y

Transferase

PDB id: 1f6y

Contents

Protein chains

258 a.a. *

Waters ×185

* Residue conservation analysis

PDB id:

1f6y

Name:

Transferase

Title:

Mad crystal structure analysis of methyltetrahydrofolate: corrinoid/iron-sulfur protein methyltransferase (metr)

Structure:

5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase. Chain: a, b. Engineered: yes

Source:

Moorella thermoacetica. Organism_taxid: 264732. Strain: atcc 39073. Cellular_location: cytoplasmic. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.209 R-free: 0.230

Authors:

T.I.Doukov,J.Seravalli,J.J.Stezowski,S.W.Ragsdale

Key ref:

T.Doukov et al. (2000). Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. Structure, 8, 817-830. PubMed id: 10997901 DOI: 10.1016/S0969-2126(00)00172-6

Date:

23-Jun-00 Release date: 31-Aug-00

Protein chains

Q46389  (ACSE_MOOTH) -  5-methyltetrahydrofolate:corrinoid/iron-sulfur protein co-methyltransferase from Moorella thermoacetica

Seq: 262 a.a.

Struc: 258 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.1.1.258 - 5-methyltetrahydrofolate:corrinoid/iron-sulfur protein
• Reaction: methyl-Co(III)-[corrinoid Fe-S protein] + (6S)-5,6,7,8-tetrahydrofolate = Co(I)-[corrinoid Fe-S protein] + (6S)-5-methyl-5,6,7,8-tetrahydrofolate + H⁺

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

Added reference

DOI no: 10.1016/S0969-2126(00)00172-6

Structure 8:817-830 (2000)

PubMed id: 10997901

Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase.

T.Doukov, J.Seravalli, J.J.Stezowski, S.W.Ragsdale.

ABSTRACT

BACKGROUND: Methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr), catalyzes a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the N5-methyl group from methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide center in another protein, the corrinoid iron-sulfur protein. MeTr is a member of a family of proteins that includes methionine synthase and methanogenic enzymes that activate the methyl group of methyltetra-hydromethano(or -sarcino)pterin. We report the first structure of a protein in this family. RESULTS: We determined the crystal structure of MeTr from Clostridium thermoaceticum at 2.2 A resolution using multiwavelength anomalous diffraction methods. The overall architecture presents a new functional class of the versatile triose phosphate isomerase (TIM) barrel fold. The MeTr tertiary structure is surprisingly similar to the crystal structures of dihydropteroate synthetases despite sharing less than 20% sequence identity. This homology permitted the methyl-H4folate binding site to be modeled. The model suggests extensive conservation of the pterin ring binding residues in the polar active sites of the methyltransferases and dihydropteroate synthetases. The most significant structural difference between these enzymes is in a loop structure above the active site. It is quite open in MeTr, where it can be modeled as the cobalamin binding site. CONCLUSIONS: The MeTr structure consists of a TIM barrel that embeds methyl-H4folate and cobamide. All related methyltransferases are predicted to fold into a similar TIM barrel pattern and have a similar pterin and cobamide binding site. The observed structure is consistent with either a 'front' (N5) or 'back' (C8a) side protonation of CH3-H4folate, a key step that enhances the electrophilic character of the methyl group, activating it for nucleophilic attack by Co(I).

Selected figure(s)

Figure 7.
Figure 7. Common structural arrangement for cobamide-dependent enzymes. (a). The cobalamin coordinates from the 1bmt structure were used to manually dock the cobalamin molecule into the TIM barrel cavity by avoiding van der Waals clashes, but minimizing N5 to Co distance. (b) Interactions between cobalamin and methylmalonyl-CoA mutase [59 and 60]. The figures were produced using QUANTA (Molecular Simulations Inc.).

The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 817-830) copyright 2000.

Figure was selected by an automated process.