2A7P

Crystal Structure of the G81A mutant of the Active Chimera of (S)-Mandelate Dehydrogenase in complex with its substrate 3-indolelactate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of the G81A mutant form of the active chimera of (S)-mandelate dehydrogenase and its complex with two of its substrates.

Sukumar, N.Dewanti, A.Merli, A.Rossi, G.L.Mitra, B.Mathews, F.S.

(2009) Acta Crystallogr.,Sect.D 65: 543-552

  • DOI: 10.1107/S0907444909010270
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • (S)-Mandelate dehydrogenase (MDH) from Pseudomonas putida, a membrane-associated flavoenzyme, catalyzes the oxidation of (S)-mandelate to benzoylformate. Previously, the structure of a catalytically similar chimera, MDH-GOX2, rendered soluble by the ...

    (S)-Mandelate dehydrogenase (MDH) from Pseudomonas putida, a membrane-associated flavoenzyme, catalyzes the oxidation of (S)-mandelate to benzoylformate. Previously, the structure of a catalytically similar chimera, MDH-GOX2, rendered soluble by the replacement of its membrane-binding segment with the corresponding segment of glycolate oxidase (GOX), was determined and found to be highly similar to that of GOX except within the substituted segments. Subsequent attempts to cocrystallize MDH-GOX2 with substrate proved unsuccessful. However, the G81A mutants of MDH and of MDH-GOX2 displayed approximately 100-fold lower reactivity with substrate and a modestly higher reactivity towards molecular oxygen. In order to understand the effect of the mutation and to identify the mode of substrate binding in MDH-GOX2, a crystallographic investigation of the G81A mutant of the MDH-GOX2 enzyme was initiated. The structures of ligand-free G81A mutant MDH-GOX2 and of its complexes with the substrates 2-hydroxyoctanoate and 2-hydroxy-3-indolelactate were determined at 1.6, 2.5 and 2.2 A resolution, respectively. In the ligand-free G81A mutant protein, a sulfate anion previously found at the active site is displaced by the alanine side chain introduced by the mutation. 2-Hydroxyoctanoate binds in an apparently productive mode for subsequent reaction, while 2-hydroxy-3-indolelactate is bound to the enzyme in an apparently unproductive mode. The results of this investigation suggest that a lowering of the polarity of the flavin environment resulting from the displacement of nearby water molecules caused by the glycine-to-alanine mutation may account for the lowered catalytic activity of the mutant enzyme, which is consistent with the 30 mV lower flavin redox potential. Furthermore, the altered binding mode of the indolelactate substrate may account for its reduced activity compared with octanoate, as observed in the crystalline state.


    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
    • 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


    Organizational Affiliation

    NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
(S)-Mandelate Dehydrogenase
A
380Pseudomonas putidaSpinacia oleracea
This entity is chimeric
Mutation(s): 1 
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
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
3IL
Query on 3IL

Download SDF File 
Download CCD File 
A
3-(INDOL-3-YL) LACTATE
(2S)-2-HYDROXY-3-(1H-INDOL-3-YL)PROPANOIC ACID
C11 H11 N O3
XGILAAMKEQUXLS-JTQLQIEISA-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: 2.2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 99.400α = 90.00
b = 99.400β = 90.00
c = 87.600γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-08-23
    Type: Advisory, Refinement description, Source and taxonomy