Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase

Tzanko Doukov, Javier Seravalli, John J. Stezowski, Stephen W. Ragsdale

Research output: Contribution to journalArticle

57 Citations (Scopus)

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 Å 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 200% 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).

Original languageEnglish (US)
Pages (from-to)817-830
Number of pages14
JournalStructure
Volume8
Issue number8
DOIs
StatePublished - Aug 15 2000

Fingerprint

Corrinoids
Methyltransferases
Pterins
Triose-Phosphate Isomerase
Cobamides
Dihydropteroate Synthase
Iron-Sulfur Proteins
Binding Sites
Catalytic Domain
Protein Methyltransferases
5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase
Carbon Cycle
Proteins
Clostridium
Enzymes
Vitamin B 12
Carbon Dioxide
Amides

Keywords

  • Carbon dioxide fixation
  • Cobalamin
  • Methyltetrahydrofolate
  • Methyltransferase
  • One-carbon metabolism

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. / Doukov, Tzanko; Seravalli, Javier; Stezowski, John J.; Ragsdale, Stephen W.

In: Structure, Vol. 8, No. 8, 15.08.2000, p. 817-830.

Research output: Contribution to journalArticle

Doukov, Tzanko ; Seravalli, Javier ; Stezowski, John J. ; Ragsdale, Stephen W. / Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase. In: Structure. 2000 ; Vol. 8, No. 8. pp. 817-830.
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T1 - Crystal structure of a methyltetrahydrofolate- and corrinoid-dependent methyltransferase

AU - Doukov, Tzanko

AU - Seravalli, Javier

AU - Stezowski, John J.

AU - Ragsdale, Stephen W.

PY - 2000/8/15

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N2 - 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 Å 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 200% 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).

AB - 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 Å 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 200% 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).

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KW - Methyltetrahydrofolate

KW - Methyltransferase

KW - One-carbon metabolism

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