1DIA

HUMAN METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE COMPLEXED WITH NADP AND INHIBITOR LY249543


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • Primary Citation of Related Structures:  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/cyclohyd ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE
A, B
306Homo sapiensGene Names: MTHFD1 (MTHFC, MTHFD)
EC: 1.5.1.5, 6.3.4.3, 3.5.4.9
Find proteins for P11586 (Homo sapiens)
Go to Gene View: MTHFD1
Go to UniProtKB:  P11586
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
L24
Query on L24

Download SDF File 
Download CCD File 
A
[[[2-AMINO-5,6,7,8-TETRAHYDRO-4-HYDROXY-PYRIDO[2,3-D]PYRIMIDIN-6-YL]-ETHYL]-PHENYL]-CARBONYL-GLUTAMIC ACID
LY249543
C21 H25 N5 O6
ZUQBAQVRAURMCL-WFASDCNBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L24Ki: 455000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.871α = 90.00
b = 136.396β = 90.00
c = 61.649γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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