3IA4

Moritella profunda dihydrofolate reductase (DHFR) in complex with NADPH and methotrexate (MTX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Are the Catalytic Properties of Enzymes from Piezophilic Organisms Pressure Adapted?

Hay, S.Evans, R.M.Levy, C.Loveridge, E.J.Wang, X.Leys, D.Allemann, R.K.Scrutton, N.S.

(2009) Chembiochem 10: 2348-2353

  • DOI: 10.1002/cbic.200900367
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the crystal structure of dihydrofolate reductase (DHFR) from the psychropiezophilic bacterium Moritella profunda, which was isolated from the deep ocean at 2 degrees C and 280 bar. The structure is typical of a chromosomal DHFR and we were ...

    We report the crystal structure of dihydrofolate reductase (DHFR) from the psychropiezophilic bacterium Moritella profunda, which was isolated from the deep ocean at 2 degrees C and 280 bar. The structure is typical of a chromosomal DHFR and we were unable to identify any obvious structural features that would suggest pressure adaptation. In particular, the core regions of the enzyme are virtually identical to those of the DHFR from the mesophile Escherichia coli. The steady-state rate at pH 9, which is limited by hydride transfer at atmospheric pressure, is roughly constant between 1 and 750 bar, falling at higher pressures. However, the value of K(M) increases with increasing pressure, and as a result k(cat)/K(M) decreases over the entire pressure range studied. Isotope effect studies showed that increasing the pressure causes a change in the rate-limiting step of the reaction. We therefore see no evidence of pressure adaptation in either the structure or the activity of this enzyme.


    Organizational Affiliation

    Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductase
A, B, C, D
162Moritella profundaMutation(s): 0 
Gene Names: dyrA
EC: 1.5.1.3
Find proteins for Q70YQ6 (Moritella profunda)
Go to UniProtKB:  Q70YQ6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTX
Query on MTX

Download SDF File 
Download CCD File 
A, B, C, D
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B, C, D
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.154 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 183.870α = 90.00
b = 44.990β = 114.82
c = 97.370γ = 90.00
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
XDSdata reduction
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-07-13 
  • Released Date: 2009-07-21 
  • Deposition Author(s): Levy, C.

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance