8UY2 | pdb_00008uy2

Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, AdoMet-bound, Inhibited (T) State

PDB DOI: https://doi.org/10.2210/pdb8UY2/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Thermochaetoides thermophila DSM 1495
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-11-12 Released: 2024-06-19
Deposition Author(s): Yamada, K., Mendoza, J., Koutmos, M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free:
0.203 (Depositor), 0.203 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of S-adenosylmethionine-dependent allosteric transition from active to inactive states in methylenetetrahydrofolate reductase.

Yamada, K., Mendoza, J., Koutmos, M.

(2024) Nat Commun 15: 5167-5167

PubMed: 38886362 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-49327-5
Primary Citation Related Structures:
8UY1, 8UY2

PubMed Abstract:
Methylenetetrahydrofolate reductase (MTHFR) is a pivotal flavoprotein connecting the folate and methionine methyl cycles, catalyzing the conversion of methylenetetrahydrofolate to methyltetrahydrofolate. Human MTHFR (hMTHFR) undergoes elaborate allosteric regulation involving protein phosphorylation and S-adenosylmethionine (AdoMet)-dependent inhibition, though other factors such as subunit orientation and FAD status remain understudied due to the lack of a functional structural model. Here, we report crystal structures of Chaetomium thermophilum MTHFR (cMTHFR) in both active (R) and inhibited (T) states. We reveal FAD occlusion by Tyr361 in the T-state, which prevents substrate interaction. Remarkably, the inhibited form of cMTHFR accommodates two AdoMet molecules per subunit. In addition, we conducted a detailed investigation of the phosphorylation sites in hMTHFR, three of which were previously unidentified. Based on the structural framework provided by our cMTHFR model, we propose a possible mechanism to explain the allosteric structural transition of MTHFR, including the impact of phosphorylation on AdoMet-dependent inhibition.

Organizational Affiliation

Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA. yamadak@umich.edu.

Macromolecule Content

Total Structure Weight: 288.66 kDa
Atom Count: 18,670
Modeled Residue Count: 2,217
Deposited Residue Count: 2,468
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylenetetrahydrofolate reductase-like protein	A, B, C, D	617	Thermochaetoides thermophila DSM 1495	Mutation(s): 1 Gene Names: CTHT_0033700 EC: 1.5.1.20
UniProt
Find proteins for G0S5U9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S5U9 Go to UniProtKB: G0S5U9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0S5U9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain E [auth A] SDF format, chain U [auth C] SDF format, chain L [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain U [auth C] MOL2 format, chain L [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain U [auth C] mmCIF format, chain L [auth B]	BA [auth D], E [auth A], L [auth B], U [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain L [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain L [auth B] Focus chain U [auth C]
SAM (Subject of Investigation/LOI) Query on SAM Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain DA [auth D] SDF format, chain CA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D]	CA [auth D] DA [auth D] F [auth A] G [auth A] M [auth B] CA [auth D], DA [auth D], F [auth A], G [auth A], M [auth B], N [auth B], V [auth C], W [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain V [auth C] Focus chain W [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain Z [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain FA [auth D] SDF format, chain EA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain FA [auth D] MOL2 format, chain EA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain FA [auth D] mmCIF format, chain EA [auth D]	AA [auth C] EA [auth D] FA [auth D] J [auth A] Q [auth B] AA [auth C], EA [auth D], FA [auth D], J [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain P [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain P [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain P [auth B]	P [auth B], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Focus chain Y [auth C] Interactions & Density Focus chain P [auth B] Focus chain Y [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain X [auth C] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain X [auth C] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain X [auth C] mmCIF format, chain I [auth A]	H [auth A], I [auth A], O [auth B], X [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain X [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]