1F0Y

L-3-HYDROXYACYL-COA DEHYDROGENASE COMPLEXED WITH ACETOACETYL-COA AND NAD+

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


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

Literature

Sequestration of the active site by interdomain shifting. Crystallographic and spectroscopic evidence for distinct conformations of L-3-hydroxyacyl-CoA dehydrogenase.

Barycki, J.J., O'Brien, L.K., Strauss, A.W., Banaszak, L.J.

(2000) J.Biol.Chem. 275: 27186-27196

  • DOI: 10.1074/jbc.M004669200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • l-3-Hydroxyacyl-CoA dehydrogenase reversibly catalyzes the conversion of l-3-hydroxyacyl-CoA to 3-ketoacyl-CoA concomitant with the reduction of NAD(+) to NADH as part of the beta-oxidation spiral. In this report, crystal structures have been solved ...

    l-3-Hydroxyacyl-CoA dehydrogenase reversibly catalyzes the conversion of l-3-hydroxyacyl-CoA to 3-ketoacyl-CoA concomitant with the reduction of NAD(+) to NADH as part of the beta-oxidation spiral. In this report, crystal structures have been solved for the apoenzyme, binary complexes of the enzyme with reduced cofactor or 3-hydroxybutyryl-CoA substrate, and an abortive ternary complex of the enzyme with NAD(+) and acetoacetyl-CoA. The models illustrate positioning of cofactor and substrate within the active site of the enzyme. Comparison of these structures with the previous model of the enzyme-NAD(+) complex reveals that although significant shifting of the NAD(+)-binding domain relative to the C-terminal domain occurs in the ternary and substrate-bound complexes, there are few differences between the apoenzyme and cofactor-bound complexes. Analysis of these models clarifies the role of key amino acids implicated in catalysis and highlights additional critical residues. Furthermore, a novel charge transfer complex has been identified in the course of abortive ternary complex formation, and its characterization provides additional insight into aspects of the catalytic mechanism of l-3-hydroxyacyl-CoA dehydrogenase.

    Related Citations: 
    • Biochemical Characterization and Crystal Structure Determination of Human Heart Short Chain L-3-Hydroxyacyl-CoA Dehydrogenase Provide Insights into Catalytic Mechanism
      Barycki, J.J.,O'Brien, L.K.,Bratt, J.M.,Zhang, R.,Sanishvili, R.,Strauss, A.W.,Banaszak, L.J.
      (1999) Biochemistry 38: 5786

    Organizational Affiliation: 

    Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-3-HYDROXYACYL-COA DEHYDROGENASE
A, B
302Homo sapiensMutation(s): 0 
Gene Names: HADH (HAD, HADHSC, SCHAD)
EC: 1.1.1.35
Find proteins for Q16836 (Homo sapiens)
Go to Gene View: HADH
Go to UniProtKB:  Q16836
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAA
Query on CAA
Download SDF File 
Download CCD File 
A, B
ACETOACETYL-COENZYME A
C25 H40 N7 O18 P3 S
OJFDKHTZOUZBOS-CITAKDKDSA-N
 Ligand Interaction
NAD
Query on NAD
Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.488α = 90.00
b = 87.971β = 90.00
c = 159.002γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
CNSphasing
CrystalCleardata scaling
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection