Structure of Human Isovaleryl-CoA Dehydrogenase at 2.6 Å Resolution:  Structural Basis for Substrate Specificity^,

Abstract

Isovaleryl-CoA dehydrogenase (IVD) belongs to an important flavoprotein family of acyl-CoA dehydrogenases that catalyze the alpha,beta-dehydrogenation of their various thioester substrates. Although enzymes from this family share similar sequences, catalytic mechanisms, and structural properties, the position of the catalytic base in the primary sequence is not conserved. E376 has been confirmed to be the catalytic base in medium-chain (MCAD) and short-chain acyl-CoA dehydrogenases and is conserved in all members of the acyl-CoA dehydrogenase family except for IVD and long-chain acyl-CoA dehydrogenase. To understand this dichotomy and to gain a better understanding of the factors important in determining substrate specificity in this enzyme family, the three-dimensional structure of human IVD has been determined. Human IVD expressed in Escherichia coli crystallizes in the orthorhombic space group P212121 with unit cell parameters a = 94.0 A, b = 97.7 A, and c = 181.7 A. The structure of IVD was solved at 2.6 A resolution by the molecular replacement method and was refined to an R-factor of 20.7% with an Rfree of 28.8%. The overall polypeptide fold of IVD is similar to that of other members of this family for which structural data are available. The tightly bound ligand found in the active site of the structure of IVD is consistent with that of CoA persulfide. The identity of the catalytic base was confirmed to be E254, in agreement with previous molecular modeling and mutagenesis studies. The location of the catalytic residue together with a glycine at position 374, which is a tyrosine in all other members of the acyl-CoA dehydrogenase family, is important for conferring branched-chain substrate specificity to IVD.

The Serratia gene cluster encoding biosynthesis of the red antibiotic, prodigiosin, shows species- and strain-dependent genome context variation

“…PigA has good sequence identity with a wide range of acylCoA dehydrogenases. Sequence alignment with human isovaleryl-CoA dehydrogenase, the crystal structure of which has been determined, showed that the majority of amino acids around the flavin and the phosphopantetheinyl moiety of CoA are conserved but the amino acids involved in binding the adenosyl group of CoA are not conserved (Tiffany et al, 1997). This supports the suggestion that the substrate for PigA is a prolyl PCP rather than prolyl-CoA.…”

Structure and DNA binding of alkylation response protein AidB

“…wrote the paper. (19), isovaleryl acyl-CoA dehydrogenase (IVD, PDB ID code 1IVH) (18), acyl-CoA oxidase II (ACO, PDB ID code 1IS2) (9), and nitroalkane oxidase (NAO, PDB ID code 2C0U) (26). AidB residues important for tetramerization and DNA binding are highlighted gray and black, respectively, and those predicted to contact DNA are marked with black triangles.…”

“…3) (10). It has been proposed that the glycine in this position in IVD allows for binding branched acyl chains (8,18). In addition to the Trp-424 steric block, the 5-Å displacement of the Glu-425 carboxylate from its normal position in ACADs (Fig.…”

Expression, purification and crystallization of two peroxisomal acyl-CoA oxidases fromArabidopsis thaliana

“…The selfrotation function has only point-groupspeci®c peaks, but the native Patterson map calculated for 10±4 A Ê data has a weak but signi®cant 9' translational symmetry peak at (0.32, 0.68, 0.61) and a 7' peak at (0.67, 0.33, 0.25). Attempts to solve the structure of ACX4 by molecular replacement using the complete structures or domains from medium-chain acyl-CoA dehydrogenase (Kim et al, 1993), buturyl-CoA dehydrogenase (Djordjevic et al, 1995), isovaleryl dehydrogenase (Tiffany et al, 1997) or shortchain acyl-CoA dehydrogenase (Battaile et al, 2002) were unsuccessful. The sequence identity between A. thaliana ACX4 and the ACADs is only $20%, while its identity to other ACXs is below 15%, making the selection of a common structural motif dif®cult.…”