3MDE

CRYSTAL STRUCTURES OF MEDIUM CHAIN ACYL-COA DEHYDROGENASE FROM PIG LIVER MITOCHONDRIA WITH AND WITHOUT SUBSTRATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate.

Kim, J.J.Wang, M.Paschke, R.

(1993) Proc.Natl.Acad.Sci.USA 90: 7523-7527

  • DOI: 10.1073/pnas.90.16.7523
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The three-dimensional structure of medium-chain acyl-CoA dehydrogenase from pig mitochondria in the native form and that of a complex of the enzyme and a substrate (product) have been solved and refined by x-ray crystallographic methods at 2.4-A reso ...

    The three-dimensional structure of medium-chain acyl-CoA dehydrogenase from pig mitochondria in the native form and that of a complex of the enzyme and a substrate (product) have been solved and refined by x-ray crystallographic methods at 2.4-A resolution to R factors of 0.172 and 0.173, respectively. The overall polypeptide folding and the quaternary structure of the tetramer are essentially unchanged upon binding of the ligand, octanoyl (octenoyl)-CoA. The ligand binds to the enzyme at the rectus (re) face of the FAD in the crevice between the two alpha-helix domains and the beta-sheet domain of the enzyme. The fatty acyl chain of the thioester substrate is buried inside of the polypeptide and the 3'-AMP moiety is close to the surface of the tetrameric enzyme molecule. The alkyl chain displaces the tightly bound water molecules found in the native enzyme and the carbonyl oxygen of the thioester interacts with the ribityl 2'-hydroxyl group of the FAD and the main-chain carbonyl oxygen of Glu-376. The C alpha--C beta of the fatty acyl moiety lies between the flavin and the gamma-carboxylate of Glu-376, supporting the role of Glu-376 as the base that abstracts the alpha proton in the alpha--beta dehydrogenation reaction catalyzed by the enzyme. Trp-166 and Met-165 are located at the sinister (si) side of the flavin ring at the surface of the enzyme, suggesting that they might be involved in the interactions with electron transferring flavoprotein. Lys-304, the prevalent mutation site found in patients with medium-chain acyl-CoA dehydrogenase deficiency, is located approximately 20 A away from the active site of the enzyme.


    Related Citations: 
    • Structure of the Medium-Chain Acyl-Coa Dehydrogenase from Pig Liver Mitochondria at 3-Angstroms Resolution
      Kim, J.-J.P.,Wu, J.
      (1988) Proc.Natl.Acad.Sci.USA 85: 6677


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MEDIUM CHAIN ACYL-COA DEHYDROGENASE
A, B
385Sus scrofaMutation(s): 0 
Gene Names: ACADM
EC: 1.3.8.7
Find proteins for P41367 (Sus scrofa)
Go to Gene View: ACADM
Go to UniProtKB:  P41367
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
CO8
Query on CO8

Download SDF File 
Download CCD File 
A, B
OCTANOYL-COENZYME A
C29 H50 N7 O17 P3 S
KQMZYOXOBSXMII-CECATXLMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 128.780α = 90.00
b = 137.250β = 90.00
c = 105.320γ = 90.00
Software Package:
Software NamePurpose
GPRLSArefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-09-30
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other