1P4C

High Resolution Structure of Oxidized Active Mutant of (S)-Mandelate Dehydrogenase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

High Resolution Structures of an Oxidized and Reduced Flavoprotein: THE WATER SWITCH IN A SOLUBLE FORM OF (S)-MANDELATE DEHYDROGENASE

Sukumar, N., Dewanti, A.R., Mitra, B., Mathews, F.S.

(2004) J.Biol.Chem. 279: 3749-3757

  • DOI: 10.1074/jbc.M310049200
  • Primary Citation of Related Structures:  
  • Also Cited By: 2A85, 2A7P, 2A7N

  • PubMed Abstract: 

    • The crystal structures of a soluble mutant of the flavoenzyme mandelate dehydrogenase (MDH) from Pseudomonas putida and of the substrate-reduced enzyme have been analyzed at 1.35-A resolution. The mutant (MDH-GOX2) is a fully active chimeric enzyme i ...

    The crystal structures of a soluble mutant of the flavoenzyme mandelate dehydrogenase (MDH) from Pseudomonas putida and of the substrate-reduced enzyme have been analyzed at 1.35-A resolution. The mutant (MDH-GOX2) is a fully active chimeric enzyme in which residues 177-215 of the membrane-bound MDH are replaced by residues 176-195 of glycolate oxidase from spinach. Both structures permit full tracing of the polypeptide backbone chain from residues 4-356, including a 4-residue segment that was disordered in an earlier study of the oxidized protein at 2.15 A resolution. The structures of MDH-GOX2 in the oxidized and reduced states are virtually identical with only a slight increase in the bending angle of the flavin ring upon reduction. The only other structural changes within the protein interior are a 10 degrees rotation of an active site tyrosine side chain, the loss of an active site water, and a significant movement of six other water molecules in the active site by 0.45 to 0.78 A. Consistent with solution studies, there is no apparent binding of either the substrate, mandelate, or the oxidation product, benzoylformate, to the reduced enzyme. The observed structural changes upon enzyme reduction have been interpreted as a rearrangement of the hydrogen bonding pattern within the active site that results from binding of a proton to the N-5 position of the anionic hydroquinone form of the reduced flavin prosthetic group. Implications for the low oxidase activity of the reduced enzyme are also discussed.

    Related Citations: 
    • Structure of an active Soluble Mutant of the Membrane- Associated (S)-Mandelate Dehydrogenase
      Sukumar, N.,Xu, Y.,Gatti, D.L.,Mitra, B.,Mathews, F.S.
      (2001) Biochemistry 40: 9870

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L(+)-Mandelate Dehydrogenase
A
380Pseudomonas putida, Spinacia oleracea
This entity is chimeric		Mutation(s): 0 
Gene Names: mdlB,
EC: 1.1.99.31 1.1.3.15
Find proteins for P20932 (Pseudomonas putida)
Go to UniProtKB:  P20932
Find proteins for P05414 (Spinacia oleracea)
Go to UniProtKB:  P05414
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMN
Query on FMN
Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
MES
Query on MES
Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.184 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 99.400α = 90.00
b = 99.400β = 90.00
c = 87.200γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-08-23
    Type: Advisory, Source and taxonomy