2R0N

The effect of a Glu370Asp mutation in Glutaryl-CoA Dehydrogenase on Proton Transfer to the Dienolate Intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The effect of a Glu370Asp mutation in glutaryl-CoA dehydrogenase on proton transfer to the dienolate intermediate.

Rao, K.S.Fu, Z.Albro, M.Narayanan, B.Baddam, S.Lee, H.J.Kim, J.J.Frerman, F.E.

(2007) Biochemistry 46: 14468-14477

  • DOI: 10.1021/bi7009597
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have determined steady-state rate constants and net rate constants for the chemical steps in the catalytic pathway catalyzed by the E370D mutant of glutaryl-CoA dehydrogenase and compared them with those of the wild-type dehydrogenase. We sought r ...

    We have determined steady-state rate constants and net rate constants for the chemical steps in the catalytic pathway catalyzed by the E370D mutant of glutaryl-CoA dehydrogenase and compared them with those of the wild-type dehydrogenase. We sought rationales for changes in these rate constants in the structure of the mutant cocrystallized with the alternate substrate, 4-nitrobutyric acid. Substitution of aspartate for E370, the catalytic base, results in a 24% decrease in the rate constant for proton abstraction at C-2 of 3-thiaglutaryl-CoA as the distance between C-2 of the ligand and the closest carboxyl oxygen at residue 370 increases from 2.9 A to 3.1 A. The net rate constant for flavin reduction due to hydride transfer from C-3 of the natural substrate, which includes proton abstraction at C-2, to N5 of the flavin decreases by 81% due to the mutation, although the distance increases only by 0.7 A. The intensities of charge-transfer bands associated with the enolate of 3-thiaglutaryl-CoA, the reductive half-reaction (reduced flavin with oxidized form of substrate), and the dienolate following decarboxylation are considerably diminished. Structural investigation suggests that the increased distance and the change in angle of the S-C1(=O)-C2 plane of the substrate with the isoalloxazine substantially alter rates of the reductive and oxidative half-reactions. This change in active site geometry also changes the position of protonation of the four carbon dienolate intermediate to produce kinetically favorable product, vinylacetyl-CoA, which is further isomerized to the thermodynamically stable normal product, crotonyl-CoA.


    Organizational Affiliation

    Department of Pediatrics, University of Colorado at Denver and Health Sciences Center, Aurora, Colorado 80045-0511, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutaryl-CoA dehydrogenase
A
394Homo sapiensMutation(s): 0 
Gene Names: GCDH
EC: 1.3.8.6
Find proteins for Q92947 (Homo sapiens)
Go to Gene View: GCDH
Go to UniProtKB:  Q92947
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
TGC
Query on TGC

Download SDF File 
Download CCD File 
A
3-thiaglutaryl-CoA
(3R,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14,19-trioxo-2,4,6-trioxa-18,21-dithia-11,15-diaza-3,5-diphosphatricosan-23-oic acid 3,5-dioxide
C25 H40 N7 O19 P3 S2
GKSSRSUPHZUOQO-ITIYDSSPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.219 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 114.650α = 90.00
b = 114.650β = 90.00
c = 126.780γ = 120.00
Software Package:
Software NamePurpose
MERLOTphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance