3NGL | pdb_00003ngl

Crystal structure of bifunctional 5,10-methylenetetrahydrofolate dehydrogenase / cyclohydrolase from Thermoplasma acidophilum

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.246 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

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Literature

Crystal structure of bifunctional 5,10-methylenetetrahydrofolate dehydrogenase/cyclohydrolase from Thermoplasma acidophilum

Lee, W.H., Sung, M.W., Kim, J.H., Kim, Y.K., Han, A., Hwang, K.Y.

(2011) Biochem Biophys Res Commun 406: 459-463

  • DOI: https://doi.org/10.1016/j.bbrc.2011.02.074
  • Primary Citation Related Structures: 
    3NGL, 3NGX

  • PubMed Abstract: 

    Folate co-enzymes play a pivotal role in one-carbon transfer cellular processes. Many eukaryotes encode the tri-functional tetrahydrofolate dehydrogenase/cyclohydrolase/synthetase (deh/cyc/syn) enzyme, which consists of a N-terminal bifunctional domain (deh/cyc) and a C-terminal monofunctional domain (syn). Here, we report the first analogous archeal enzyme structures, for the bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase from Thermoplasma acidophilum (TaMTHFDC) as the native protein and also as its NADP complex. The TaMTHFDC structure is a dimer with a polar interface, as well as a NADP binding site that shows minor conformational change. The orientations of the residues in the NADP binding site do not change on ligand binding, incorporating three water molecules which are hydrogen bonded with phosphate groups of NADP in the structure of the complex. Our structural information will contribute to an improved understanding of the basis of THF and one-carbon metabolism.

    • Organizational Affiliation: 
    • Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, South Korea.

Macromolecule Content 

  • Total Structure Weight: 62.81 kDa 
  • Atom Count: 4,437 
  • Modeled Residue Count: 549 
  • Deposited Residue Count: 552 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional protein folDA,
B [auth C]		276Thermoplasma acidophilumMutation(s): 0 
EC: 1.5.1.5 (PDB Primary Data), 3.5.4.9 (PDB Primary Data)
UniProt
Find proteins for Q05213 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q05213 
Go to UniProtKB:  Q05213
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05213
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.246 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.333α = 90
b = 52.868β = 97.57
c = 86.099γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations