5ZF1 | pdb_00005zf1

Molecular structure of a novel 5,10-methylenetetrahydrofolate dehydrogenase from the silkworm, Bombyx mori

• PDB DOI: https://doi.org/10.2210/pdb5ZF1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bombyx mori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-02 Released: 2019-01-23 
• Deposition Author(s): Haque, R., Higashiura, A., Nakagawa, A., Yamamoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.241 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Molecular structure of a 5,10-methylenetetrahydrofolate dehydrogenase from the silkwormBombyx mori.

Haque, M.R., Higashiura, A., Nakagawa, A., Hirowatari, A., Furuya, S., Yamamoto, K.

(2019) FEBS Open Bio 9: 618-628

• PubMed: 30984537 
• DOI: https://doi.org/10.1002/2211-5463.12595
• Primary Citation Related Structures: 
  5ZF1


• PubMed Abstract: 
  

  The enzyme 5,10-methylenetetrahydrofolate dehydrogenase (MTHFD) is essential for the production of certain amino acids (glycine, serine, and methionine) and nucleic acids (thymidylate and purine). Here, we identified a cDNA encoding this enzyme from the silkworm Bombyx mori . The recombinant B. mori MTHFD (bmMTHFD) expressed in Escherichia coli recognized 5,10-methylenetetrahydrofolate and 5,10-methenyltetrahydrofolate as substrate in the presence of NADP ⁺ as well as NAD ⁺ . The bmMTHFD structure was determined at a resolution of 1.75 Å by X-ray crystallography. Site-directed mutagenesis indicated that the amino acid residue Tyr49 contributed to its catalytic activity. Our findings provide insight into the mechanism underlying the activity of MTHFD from B. mori and potentially other insects and may therefore facilitate the development of inhibitors specific to MTHFD as insecticides.

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Organizational Affiliation: 
• Department of Bioscience and Biotechnology Kyushu University Graduate School Fukuoka Japan.
Institute for Protein Research Osaka University Suita Japan.
Present address: Department of Virology Graduate School of Biomedical and Health Sciences Hiroshima University Hiroshima Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 66.09 kDa 
• Atom Count: 4,821 
• Modeled Residue Count: 578 
• Deposited Residue Count: 602 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,10-methylenetetrahydrofolate dehydrogenase	A, B	301	Bombyx mori	Mutation(s): 0  Gene Names: LOC101741628

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.241 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.789	α = 90
b = 89.789	β = 90
c = 127.306	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Haque, R., Higashiura, A., Nakagawa, A., Yamamoto, K.

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-05-01
  Changes: Data collection, Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references