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 
  • R-Value Observed: 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:  
    1P4C, 1P5B

  • 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 in which residues 177-215 of the membrane-bound MDH are replaced by residues 176-195 of glycolate oxidase from spinach ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L(+)-Mandelate DehydrogenaseA380Pseudomonas putidaSpinacia oleraceaMutation(s): 0 
Gene Names: mdlB
EC: 1.1.3.15 (UniProt), 1.1.99.31 (UniProt)
Find proteins for P20932 (Pseudomonas putida)
Explore P20932 
Go to UniProtKB:  P20932
Find proteins for P05414 (Spinacia oleracea)
Explore P05414 
Go to UniProtKB:  P05414
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
MES
Query on MES

Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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 
  • R-Value Observed: 0.184 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.4α = 90
b = 99.4β = 90
c = 87.2γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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