PDBsum entry 1jqi

Oxidoreductase

PDB id: 1jqi

Contents

Protein chains

384 a.a. *

Ligands

CAA ×2

FAD ×2

Waters ×260

* Residue conservation analysis

PDB id:

1jqi

Name:

Oxidoreductase

Title:

Crystal structure of rat short chain acyl-coa dehydrogenase complexed with acetoacetyl-coa

Structure:

Short chain acyl-coa dehydrogenase. Chain: a, b. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.25Å R-factor: 0.168 R-free: 0.206

Authors:

K.P.Battaile,J.Molin-Case,R.Paschke,M.Wang,D.Bennett,J.Vockley,J.- J.P.Kim

Key ref:

K.P.Battaile et al. (2002). Crystal structure of rat short chain acyl-CoA dehydrogenase complexed with acetoacetyl-CoA: comparison with other acyl-CoA dehydrogenases. J Biol Chem, 277, 12200-12207. PubMed id: 11812788 DOI: 10.1074/jbc.M111296200

Date:

07-Aug-01 Release date: 13-Feb-02

Protein chains

P15651  (ACADS_RAT) -  Short-chain specific acyl-CoA dehydrogenase, mitochondrial from Rattus norvegicus

Seq: 412 a.a.

Struc: 384 a.a.

Enzyme reactions

• Enzyme class: E.C.1.3.8.1 - short-chain acyl-CoA dehydrogenase.
• Reaction: a short-chain 2,3-saturated fatty acyl-CoA + oxidized [electron-transfer flavoprotein] + H⁺ = a short-chain (2E)-enoyl-CoA + reduced [electron- transfer flavoprotein]

Butanoyl-CoA (Bound ligand (Het Group name = CAA) matches with 98.15% similarity) + electron-transfer flavoprotein = 2-butenoyl-CoA + reduced electron-transfer flavoprotein

• Cofactor: FAD

FAD (Bound ligand (Het Group name = FAD) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M111296200

J Biol Chem 277:12200-12207 (2002)

PubMed id: 11812788

Crystal structure of rat short chain acyl-CoA dehydrogenase complexed with acetoacetyl-CoA: comparison with other acyl-CoA dehydrogenases.

K.P.Battaile, J.Molin-Case, R.Paschke, M.Wang, D.Bennett, J.Vockley, J.J.Kim.

ABSTRACT

The acyl-CoA dehydrogenases are a family of flavin adenine dinucleotide-containing enzymes that catalyze the first step in the beta-oxidation of fatty acids and catabolism of some amino acids. They exhibit high sequence identity and yet are quite specific in their substrate binding. Short chain acyl-CoA dehydrogenase has maximal activity toward butyryl-CoA and negligible activity toward substrates longer than octanoyl-CoA. The crystal structure of rat short chain acyl-CoA dehydrogenase complexed with the inhibitor acetoacetyl-CoA has been determined at 2.25 A resolution. Short chain acyl-CoA dehydrogenase is a homotetramer with a subunit mass of 43 kDa and crystallizes in the space group P321 with a = 143.61 A and c = 77.46 A. There are two monomers in the asymmetric unit. The overall structure of short chain acyl-CoA dehydrogenase is very similar to those of medium chain acyl-CoA dehydrogenase, isovaleryl-CoA dehydrogenase, and bacterial short chain acyl-CoA dehydrogenase with a three-domain structure composed of N- and C-terminal alpha-helical domains separated by a beta-sheet domain. Comparison to other acyl-CoA dehydrogenases has provided additional insight into the basis of substrate specificity and the nature of the oxidase activity in this enzyme family. Ten reported pathogenic human mutations and two polymorphisms have been mapped onto the structure of short chain acyl-CoA dehydrogenase. None of the mutations directly affect the binding cavity or intersubunit interactions.

Selected figure(s)

Figure 1.
Fig. 1. The overall polypeptide folding of the SCAD monomer. A, ribbon diagram of the SCAD monomer. Helices are labeled A-K and -strands 1-7. FAD is rendered in yellow and acetoacetyl-CoA in green. B, stereo view of overlay of SCAD (blue), MCAD (red), bSCAD (green), and IVD (gray). FAD is rendered in yellow and acetoacetyl-CoA in indigo. Orientation of the monomer is the same as in A. The figure was generated using Molscript (44) and Raster3D (45).

Figure 3.
Fig. 3. Stereo diagram of acetoacetyl-CoA and amino acid residues involved in binding the CoA moiety in SCAD. Acetoacetyl-CoA is rendered in ball-and-stick format, and amino acids are rendered as sticks. The acetoacetyl-CoA is "outside" and all amino acids are "inside" of the molecular surface of the enzyme. The molecular surface was generated with a 1.4-Å probe using the program Grasp (46). Molscript (44) and Raster3D (45) were used to render the image.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 12200-12207) copyright 2002.

Figures were selected by an automated process.