1DIB

HUMAN METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE COMPLEXED WITH NADP AND INHIBITOR LY345899


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6ECQ


Literature

Structures of three inhibitor complexes provide insight into the reaction mechanism of the human methylenetetrahydrofolate dehydrogenase/cyclohydrolase.

Schmidt, A.Wu, H.MacKenzie, R.E.Chen, V.J.Bewly, J.R.Ray, J.E.Toth, J.E.Cygler, M.

(2000) Biochemistry 39: 6325-6335

  • DOI: 10.1021/bi992734y
  • Primary Citation of Related Structures:  
    1DIA, 1DIB, 1DIG

  • PubMed Abstract: 
  • Enzymes involved in tetrahydrofolate metabolism are of particular pharmaceutical interest, as their function is crucial for amino acid and DNA biosynthesis. The crystal structure of the human cytosolic methylenetetrahydrofolate dehydrogenase/cyclohydrolase (DC301) domain of a trifunctional enzyme has been determined previously with a bound NADP cofactor ...

    Enzymes involved in tetrahydrofolate metabolism are of particular pharmaceutical interest, as their function is crucial for amino acid and DNA biosynthesis. The crystal structure of the human cytosolic methylenetetrahydrofolate dehydrogenase/cyclohydrolase (DC301) domain of a trifunctional enzyme has been determined previously with a bound NADP cofactor. While the substrate binding site was identified to be localized in a deep and rather hydrophobic cleft at the interface between two protein domains, the unambiguous assignment of catalytic residues was not possible. We succeeded in determining the crystal structures of three ternary DC301/NADP/inhibitor complexes. Investigation of these structures followed by site-directed mutagenesis studies allowed identification of the amino acids involved in catalysis by both enzyme activities. The inhibitors bind close to Lys56 and Tyr52, residues of a strictly conserved motif for active sites in dehydrogenases. While Lys56 is in a good position for chemical interaction with the substrate analogue, Tyr52 was found stacking against the inhibitors' aromatic rings and hence seems to be more important for proper positioning of the ligand than for catalysis. Also, Ser49 and/or Cys147 were found to possibly act as an activator for water in the cyclohydrolase step. These and the other residues (Gln100 and Asp125), with which contacts are made, are strictly conserved in THF dehydrogenases. On the basis of structural and mutagenesis data, we propose a reaction mechanism for both activities, the dehydrogenase and the cyclohydrolase.


    Related Citations: 
    • The 3-D Structure of a Folate-Dependent Dehydrogenase/Cyclohydrolase Bifunctional Enzyme at 1.5 A Resolution
      Allaire, M., Li, Y., MacKenzie, R.E., Cygler, M.
      (1998) Structure 6: 173

    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, Montreal Joint Centre for Structural Biology, Montreal, Quebec H4P 2R2 Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASEA, B306Homo sapiensMutation(s): 0 
Gene Names: MTHFD1MTHFCMTHFD
EC: 1.5.1.5 (PDB Primary Data), 3.5.4.9 (PDB Primary Data), 6.3.4.3 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11586 (Homo sapiens)
Explore P11586 
Go to UniProtKB:  P11586
PHAROS:  P11586
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
L34 (Subject of Investigation/LOI)
Query on L34

Download Ideal Coordinates CCD File 
D [auth A]4-(7-AMINO-9-HYDROXY-1-OXO-3,3A,4,5-TETRAHYDRO-2,5,6,8,9B-PENTAAZA-CYCLOPENTA[A]NAPHTHALEN-2-YL)-PHENYLCARBONYL-GLUTAMI C ACID
C20 H21 N7 O7
JSNFRYBHBVDHSG-NEPJUHHUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.49α = 90
b = 136.37β = 90
c = 61.38γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Advisory, Experimental preparation