+
Open data
-
Basic information
Entry | Database: PDB / ID: 8qa6 | ||||||
---|---|---|---|---|---|---|---|
Title | MTHFR + SAM inhibited state | ||||||
![]() | Methylenetetrahydrofolate reductase (NADPH) | ||||||
![]() | FLAVOPROTEIN / Inhibited / allosteric / folate / S-Adenosylmethionin | ||||||
Function / homology | ![]() methylenetetrahydrofolate reductase (NADPH) / response to vitamin B2 / methylenetetrahydrofolate reductase (NADPH) activity / methylenetetrahydrofolate reductase (NAD(P)H) activity / methionine metabolic process / modified amino acid binding / homocysteine metabolic process / heterochromatin organization / S-adenosylmethionine metabolic process / Metabolism of folate and pterines ...methylenetetrahydrofolate reductase (NADPH) / response to vitamin B2 / methylenetetrahydrofolate reductase (NADPH) activity / methylenetetrahydrofolate reductase (NAD(P)H) activity / methionine metabolic process / modified amino acid binding / homocysteine metabolic process / heterochromatin organization / S-adenosylmethionine metabolic process / Metabolism of folate and pterines / methionine biosynthetic process / response to folic acid / tetrahydrofolate interconversion / response to amino acid / response to interleukin-1 / FAD binding / neural tube closure / NADP binding / flavin adenine dinucleotide binding / response to hypoxia / response to xenobiotic stimulus / protein-containing complex binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å | ||||||
![]() | Blomgren, L.K.M. / Yue, W.W. / Froese, D.S. / McCorvie, T.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Dynamic inter-domain transformations mediate the allosteric regulation of human 5, 10-methylenetetrahydrofolate reductase. Authors: Linnea K M Blomgren / Melanie Huber / Sabrina R Mackinnon / Céline Bürer / Arnaud Baslé / Wyatt W Yue / D Sean Froese / Thomas J McCorvie / ![]() ![]() Abstract: 5,10-methylenetetrahydrofolate reductase (MTHFR) commits folate-derived one-carbon units to generate the methyl-donor S-adenosyl-L-methionine (SAM). Eukaryotic MTHFR appends to the well-conserved ...5,10-methylenetetrahydrofolate reductase (MTHFR) commits folate-derived one-carbon units to generate the methyl-donor S-adenosyl-L-methionine (SAM). Eukaryotic MTHFR appends to the well-conserved catalytic domain (CD) a unique regulatory domain (RD) that confers feedback inhibition by SAM. Here we determine the cryo-electron microscopy structures of human MTHFR bound to SAM and its demethylated product S-adenosyl-L-homocysteine (SAH). In the active state, with the RD bound to a single SAH, the CD is flexible and exposes its active site for catalysis. However, in the inhibited state the RD pocket is remodelled, exposing a second SAM-binding site that was previously occluded. Dual-SAM bound MTHFR demonstrates a substantially rearranged inter-domain linker that reorients the CD, inserts a loop into the active site, positions Tyr404 to bind the cofactor FAD, and blocks substrate access. Our data therefore explain the long-distance regulatory mechanism of MTHFR inhibition, underpinned by the transition between dual-SAM and single-SAH binding in response to cellular methylation status. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 428.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 354.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 18300MC ![]() 8qa4C ![]() 8qa5C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 75461.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SAM / #3: Chemical | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Human 5,10-methylenetetrahydrofolate reductase in complex with S-Adenosyl-L-Methionine Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.15 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 Details: 20 mM HEPES, pH 7.5, 150 mM NaCl, 5 mM S-Adenosyl-L-Methionine, filter sterilised |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Au-flat 1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-
Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
---|---|
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 240000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 6.17 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 2394 |
-
Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 882000 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135192 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 105.2 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coeficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|