Structure of armadillo ACBP: a new member of the acyl-CoA-binding protein family

Abstract

PDB Reference: armadillo ACBP, 2fdq, r2fdqsf.The X-ray structure of the tetragonal form of apo acyl-CoA-binding protein (ACBP) from the Harderian gland of the South American armadillo Chaetophractus villosus has been solved. ACBP is a carrier for activated long-chain fatty acids and has been associated with many aspects of lipid metabolism. Its secondary structure is highly similar to that of the corresponding form of bovine ACBP and exhibits the unique flattened -helical bundle (up-down-down-up) motif reported for animal, yeast and insect ACBPs. Conformational differences are located in loops and turns, although these structural differences do not suffice to account for features that could be related to the unusual biochemistry and lipid metabolism of the Harderian gland.

Prediction of the most favorable configuration in the ACBP–membrane interaction based on electrostatic calculations

“…1 shows the crystal structure of ACBP from the armadillo Harderian gland (HgACBP) surrounded by surfaces representing the electrostatic properties (see Results and discussion). The crystal structure shown in ribbons is very similar to that of other ACBPs [19][20][21][22][23]. The secondary structure of HgACBP reveals the presence of four -helices, Al (Glu4-Leul5), A2 (Asp21-Val36), A3 (Gly51-Lys62), and A4 (Ser65-Tyr84) folded into an up-down-down-up helix with a loop between the A2 and A3 -helices.…”

“…Therefore, no internal degrees of freedom (i.e., flexibility of lateral chains, chemical reactions) were taken into account. HgACBP coordinates were obtained from RCSB Protein Data Bank (PDBID 2FDQ, [23]). Membrane coordinates were computationally generated snapshots and equilibrated by molecular dynamics procedures as follow.…”

“…The amino acid sequences of over thirty ACBPs, from protozoans, yeasts, plants, insects, reptiles, amphibians, fishes, and mammals, are already known. At this moment, the three-dimensional structure of liver bovine (bovACBP, [19]) (PDBID 2ABD), yeast (yACBP, [20]) (PDBID 1ST7), Plasmodium falciparum (PfmACBP, [21]) (PDBID 1HBK), human liver (hLACBP, [22]) (PDBID 2FJ9), and armadillo Harderian gland (HgACBP, [23]) (PDBID 2FDQ) ACBPs are available, and all of them are structurally homologous. Fig.…”

A hydrophobic loop in acyl-CoA binding protein is functionally important for binding to palmitoyl-coenzyme A: A molecular dynamics study

“…The setup of the simulation system consist in one chain (86 amino acids) from HgACBP structure (PDB code 2FDQ) [7] and one molecule of PlyCoA, extracted manually from the complex structure (PDB code 1NVL).…”

“…1NVL 1 ), X-ray bovine [6] (PDB accession no. 1HB8) and XRay Armadillo Harderian Gland ACBP (HgACBP) [7] (PDB accession no. 2FDQ).…”