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PDBsum entry 1jqi

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1jqi
Jmol
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 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.Vockl 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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P15651  (ACADS_RAT) -  Short-chain specific acyl-CoA dehydrogenase, mitochondrial
Seq:
Struc:
412 a.a.
384 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.3.8.1  - Short-chain acyl-CoA dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Butanoyl-CoA + electron-transfer flavoprotein = 2-butenoyl-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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   4 terms 
  Biological process     metabolic process   10 terms 
  Biochemical function     oxidoreductase activity     6 terms  

 

 
    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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19703103 T.J.Erb, G.Fuchs, and B.E.Alber (2009).
(2S)-Methylsuccinyl-CoA dehydrogenase closes the ethylmalonyl-CoA pathway for acetyl-CoA assimilation.
  Mol Microbiol, 73, 992.  
19639238 Z.Swigonová, A.W.Mohsen, and J.Vockley (2009).
Acyl-CoA dehydrogenases: Dynamic history of protein family evolution.
  J Mol Evol, 69, 176-193.  
18296637 J.I.Yeh, U.Chinte, and S.Du (2008).
Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism.
  Proc Natl Acad Sci U S A, 105, 3280-3285.
PDB codes: 2qcu 2r45 2r46 2r4e 2r4j
17656140 L.A.Maggio-Hall, P.Lyne, J.A.Wolff, and N.P.Keller (2008).
A single acyl-CoA dehydrogenase is required for catabolism of isoleucine, valine and short-chain fatty acids in Aspergillus nidulans.
  Fungal Genet Biol, 45, 180-189.  
18977676 R.Jethva, M.J.Bennett, and J.Vockley (2008).
Short-chain acyl-coenzyme A dehydrogenase deficiency.
  Mol Genet Metab, 95, 195-200.  
18227065 R.P.McAndrew, Y.Wang, A.W.Mohsen, M.He, J.Vockley, and J.J.Kim (2008).
Structural basis for substrate fatty acyl chain specificity: crystal structure of human very-long-chain acyl-CoA dehydrogenase.
  J Biol Chem, 283, 9435-9443.
PDB code: 3b96
17374501 E.S.Goetzman, Y.Wang, M.He, A.W.Mohsen, B.K.Ninness, and J.Vockley (2007).
Expression and characterization of mutations in human very long-chain acyl-CoA dehydrogenase using a prokaryotic system.
  Mol Genet Metab, 91, 138-147.  
17999356 S.Gobin-Limballe, F.Djouadi, F.Aubey, S.Olpin, B.S.Andresen, S.Yamaguchi, H.Mandel, T.Fukao, J.P.Ruiter, R.J.Wanders, R.McAndrew, J.J.Kim, and J.Bastin (2007).
Genetic basis for correction of very-long-chain acyl-coenzyme A dehydrogenase deficiency by bezafibrate in patient fibroblasts: toward a genotype-based therapy.
  Am J Hum Genet, 81, 1133-1143.  
16735577 D.Binns, T.Januszewski, Y.Chen, J.Hill, V.S.Markin, Y.Zhao, C.Gilpin, K.D.Chapman, R.G.Anderson, and J.M.Goodman (2006).
An intimate collaboration between peroxisomes and lipid bodies.
  J Cell Biol, 173, 719-731.  
16128823 L.P.O'Reilly, B.S.Andresen, and P.C.Engel (2005).
Two novel variants of human medium chain acyl-CoA dehydrogenase (MCAD). K364R, a folding mutation, and R256T, a catalytic-site mutation resulting in a well-folded but totally inactive protein.
  FEBS J, 272, 4549-4557.  
16342946 S.Bhattacharyya, S.Ma, M.T.Stankovich, D.G.Truhlar, and J.Gao (2005).
Potential of mean force calculation for the proton and hydride transfer reactions catalyzed by medium-chain acyl-CoA dehydrogenase: effect of mutations on enzyme catalysis.
  Biochemistry, 44, 16549-16562.  
15272176 A.Nagpal, M.P.Valley, P.F.Fitzpatrick, and A.M.Orville (2004).
Crystallization and preliminary analysis of active nitroalkane oxidase in three crystal forms.
  Acta Crystallogr D Biol Crystallogr, 60, 1456-1460.  
14728675 J.J.Kim, and R.Miura (2004).
Acyl-CoA dehydrogenases and acyl-CoA oxidases. Structural basis for mechanistic similarities and differences.
  Eur J Biochem, 271, 483-493.  
15159576 L.Pedersen, and A.Henriksen (2004).
Expression, purification and crystallization of two peroxisomal acyl-CoA oxidases from Arabidopsis thaliana.
  Acta Crystallogr D Biol Crystallogr, 60, 1125-1128.  
14728674 N.Gregersen, P.Bross, and B.S.Andresen (2004).
Genetic defects in fatty acid beta-oxidation and acyl-CoA dehydrogenases. Molecular pathogenesis and genotype-phenotype relationships.
  Eur J Biochem, 271, 470-482.  
12936980 M.G.Thomas, Y.A.Chan, and S.G.Ozanick (2003).
Deciphering tuberactinomycin biosynthesis: isolation, sequencing, and annotation of the viomycin biosynthetic gene cluster.
  Antimicrob Agents Chemother, 47, 2823-2830.  
12220177 T.V.Nguyen, C.Riggs, D.Babovic-Vuksanovic, Y.S.Kim, J.F.Carpenter, T.P.Burghardt, N.Gregersen, and J.Vockley (2002).
Purification and characterization of two polymorphic variants of short chain acyl-CoA dehydrogenase reveal reduction of catalytic activity and stability of the Gly185Ser enzyme.
  Biochemistry, 41, 11126-11133.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.