5ZF1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1002/2211-5463.12595
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Bioscience and Biotechnology Kyushu University Graduate School Fukuoka Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5,10-methylenetetrahydrofolate dehydrogenase
A, B
301Bombyx moriMutation(s): 0 
Gene Names: LOC101741628
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.789α = 90
b = 89.789β = 90
c = 127.306γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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