6FCX

Structure of human 5,10-methylenetetrahydrofolate reductase (MTHFR)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the regulation of human 5,10-methylenetetrahydrofolate reductase by phosphorylation and S-adenosylmethionine inhibition.

Froese, D.S.Kopec, J.Rembeza, E.Bezerra, G.A.Oberholzer, A.E.Suormala, T.Lutz, S.Chalk, R.Borkowska, O.Baumgartner, M.R.Yue, W.W.

(2018) Nat Commun 9: 2261-2261

  • DOI: https://doi.org/10.1038/s41467-018-04735-2
  • Primary Citation of Related Structures:  
    6FCX, 6FNU

  • PubMed Abstract: 

    The folate and methionine cycles are crucial for biosynthesis of lipids, nucleotides and proteins, and production of the methyl donor S-adenosylmethionine (SAM). 5,10-methylenetetrahydrofolate reductase (MTHFR) represents a key regulatory connection between these cycles, generating 5-methyltetrahydrofolate for initiation of the methionine cycle, and undergoing allosteric inhibition by its end product SAM. Our 2.5 Å resolution crystal structure of human MTHFR reveals a unique architecture, appending the well-conserved catalytic TIM-barrel to a eukaryote-only SAM-binding domain. The latter domain of novel fold provides the predominant interface for MTHFR homo-dimerization, positioning the N-terminal serine-rich phosphorylation region near the C-terminal SAM-binding domain. This explains how MTHFR phosphorylation, identified on 11 N-terminal residues (16 in total), increases sensitivity to SAM binding and inhibition. Finally, we demonstrate that the 25-amino-acid inter-domain linker enables conformational plasticity and propose it to be a key mediator of SAM regulation. Together, these results provide insight into the molecular regulation of MTHFR.


  • Organizational Affiliation

    Division of Metabolism and Children's Research Center, University Children's Hospital, CH-8032, Zürich, Switzerland. sean.froese@kispi.uzh.ch.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methylenetetrahydrofolate reductase
A, B
615Homo sapiensMutation(s): 2 
Gene Names: MTHFR
EC: 1.5.1.20 (PDB Primary Data), 1.5.1.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42898 (Homo sapiens)
Explore P42898 
Go to UniProtKB:  P42898
PHAROS:  P42898
GTEx:  ENSG00000177000 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42898
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.337α = 90
b = 127.942β = 90
c = 147.015γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXCDphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom106169/ZZ14/Z

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references