8UY1 | pdb_00008uy1

Methylenetetrahydrofolate reductase from Chaetomium thermophilum DSM 1495, Active (R) State

• PDB DOI: https://doi.org/10.2210/pdb8UY1/pdb

• Classification: OXIDOREDUCTASE
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free: 
  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: in silico

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 
• 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.

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Organizational Affiliation: 
• Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA. [e-mail].
Program in Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA. [e-mail].
Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA. [e-mail].
Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA. [e-mail].
Program in Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 284.77 kDa 
• Atom Count: 19,297 
• Modeled Residue Count: 2,363 
• Deposited Residue Count: 2,468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylenetetrahydrofolate reductase-like protein	A [auth D], B [auth A], C [auth B], D [auth C]	617	Thermochaetoides thermophila DSM 1495	Mutation(s): 3  Gene Names: CTHT_0033700
UniProt
Find proteins for G0S5U9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S5U9  Go to UniProtKB:  G0S5U9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	E [auth D], F [auth A], G [auth B], H [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.49 Å
• R-Value Free:  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.972	α = 90
b = 151.38	β = 90
c = 188.048	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MrBUMP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Yamada, K., Mendoza, J., Koutmos, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1945174

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release
  
• Version 1.1: 2024-07-03
  Changes: Database references