4M6K

Crystal structure of human dihydrofolate reductase (DHFR) bound to NADP+ and folate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Divergent evolution of protein conformational dynamics in dihydrofolate reductase.

Bhabha, G.Ekiert, D.C.Jennewein, M.Zmasek, C.M.Tuttle, L.M.Kroon, G.Dyson, H.J.Godzik, A.Wilson, I.A.Wright, P.E.

(2013) Nat Struct Mol Biol 20: 1243-1249

  • DOI: 10.1038/nsmb.2676
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Molecular evolution is driven by mutations, which may affect the fitness of an organism and are then subject to natural selection or genetic drift. Analysis of primary protein sequences and tertiary structures has yielded valuable insights into the e ...

    Molecular evolution is driven by mutations, which may affect the fitness of an organism and are then subject to natural selection or genetic drift. Analysis of primary protein sequences and tertiary structures has yielded valuable insights into the evolution of protein function, but little is known about the evolution of functional mechanisms, protein dynamics and conformational plasticity essential for activity. We characterized the atomic-level motions across divergent members of the dihydrofolate reductase (DHFR) family. Despite structural similarity, Escherichia coli and human DHFRs use different dynamic mechanisms to perform the same function, and human DHFR cannot complement DHFR-deficient E. coli cells. Identification of the primary-sequence determinants of flexibility in DHFRs from several species allowed us to propose a likely scenario for the evolution of functionally important DHFR dynamics following a pattern of divergent evolution that is tuned by cellular environment.


    Organizational Affiliation

    1] Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA. [2] Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California, USA. [3].



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A
187Homo sapiensMutation(s): 0 
Gene Names: DHFR
EC: 1.5.1.3
Find proteins for P00374 (Homo sapiens)
Go to UniProtKB:  P00374
NIH Common Fund Data Resources
PHAROS  P00374
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
FOL
Query on FOL

Download CCD File 
A
FOLIC ACID
C19 H19 N7 O6
OVBPIULPVIDEAO-LBPRGKRZSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.213α = 90
b = 68.213β = 90
c = 160.163γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-10-16
    Changes: Database references
  • Version 1.2: 2013-11-20
    Changes: Database references