1BUC

THREE-DIMENSIONAL STRUCTURE OF BUTYRYL-COA DEHYDROGENASE FROM MEGASPHAERA ELSDENII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of butyryl-CoA dehydrogenase from Megasphaera elsdenii.

Djordjevic, S.Pace, C.P.Stankovich, M.T.Kim, J.J.

(1995) Biochemistry 34: 2163-2171


  • PubMed Abstract: 
  • The crystal structure of butyryl-CoA dehydrogenase (BCAD) from Megasphaera elsdenii complexed with acetoacetyl-CoA has been solved at 2.5 A resolution. The enzyme crystallizes in the P422 space group with cell dimensions a = b = 107.76 A and c = 153. ...

    The crystal structure of butyryl-CoA dehydrogenase (BCAD) from Megasphaera elsdenii complexed with acetoacetyl-CoA has been solved at 2.5 A resolution. The enzyme crystallizes in the P422 space group with cell dimensions a = b = 107.76 A and c = 153.67 A. BCAD is a bacterial analog of short chain acyl-CoA dehydrogenase from mammalian mitochondria. Mammalian acyl-CoA dehydrogenases are flavin adenine dinucleotide (FAD)-containing enzymes that catalyze the first step in the beta-oxidation of fatty acids. Although specific for substrate chain lengths, they exhibit high sequence homology. The structure of BCAD was solved by the molecular replacement method using the atomic coordinates of pig liver medium chain acyl-CoA dehydrogenase (MCAD). The structure was refined to an R-factor of 19.3%. The overall polypeptide fold of BCAD is similar to that of MCAD. E367 in BCAD is at the same position and in a similar conformation as the catalytic base in MCAD, E376. The main enzymatic differences between BCAD and MCAD are their substrate specificities and the significant oxygen reactivity exhibited by BCAD but not by MCAD. The substrate binding cavity of BCAD is relatively shallow compared to that of MCAD, as consequences of both a single amino acid insertion and differences in the side chains of the helices that make the binding site. The si-face of the FAD in BCAD is more exposed to solvent than that in MCAD. Therefore solvation can stabilize the superoxide anion and considerably increase the rate of oxidation of reduced flavin in the bacterial enzyme.


    Organizational Affiliation

    Department of Biochemistry, Medical College of Wisconsin, Milwaukee 53226.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BUTYRYL-COA DEHYDROGENASE
A, B
383Megasphaera elsdeniiEC: 1.3.8.1
Find proteins for Q06319 (Megasphaera elsdenii)
Go to UniProtKB:  Q06319
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
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.193 
  • Space Group: P 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 107.800α = 90.00
b = 107.800β = 90.00
c = 153.700γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-04-20
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance