Binding site differences revealed by crystal structures of Plasmodium falciparum and bovine acyl-CoA binding protein

Aalten, Daan M. F. van; Milne, Kenneth G.; Zou, Jiezhong; Kleywegt, Gerard J.; Bergfors, Terese; Ferguson, Michael A. J.; Knudsen, Jens; Jones, T. Alwyn

doi:10.1006/jmbi.2001.4749

Cited by 59 publications

(56 citation statements)

References 27 publications

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“…Rather, it reflects the competitive binding between ACBP and Lipidex 1000 (Rasmussen et al, 1994). The K d values determined by fluorescence or dialyser-based methods are typically lower, in the range of 1-10 nM (Chao et al, 2002;Milne & Ferguson, 2000;van Aalten et al, 2001;Wadum et al, 2002). On the other hand, although Lipidex 1000 cannot be used to assess the true binding affinity of ACBPs, this method can be used as a qualitative assessment, such as the ligand competition assay.…”

Section: Discussionmentioning

confidence: 99%

“…Although ACBPs are capable of binding mediumto long-chain fatty acyl-CoA esters, they may vary in their substrate preference and binding affinities. For example, the highest affinities of ACBPs from bovines (liver) and trypanosomes (or P. falciparum) are C18 stearoyl-and C14 lauroyl-CoA, respectively (Milne & Ferguson, 2000;van Aalten et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

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Functional characterization of a fatty acyl-CoA-binding protein (ACBP) from the apicomplexan Cryptosporidium parvum

2006

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In this paper, the identification and functional analysis of a fatty acyl-CoA-binding protein (ACBP) gene from the opportunistic protist Cryptosporidium parvum are described. The CpACBP1 gene encodes a protein of 268 aa that is three times larger than typical ACBPs (i.e. ∼90 aa) of humans and animals. Sequence analysis indicated that the CpACBP1 protein consists of an N-terminal ACBP domain (∼90 aa) and a C-terminal ankyrin repeat sequence (∼170 aa). The entire CpACBP1 ORF was engineered into a maltose-binding protein fusion system and expressed as a recombinant protein for functional analysis. Acyl-CoA-binding assays clearly revealed that the preferred binding substrate for CpACBP1 is palmitoyl-CoA. RT-PCR, Western blotting and immunolabelling analyses clearly showed that the CpACBP1 gene is mainly expressed during the intracellular developmental stages and that the level increases during parasite development. Immunofluorescence microscopy showed that CpACBP1 is associated with the parasitophorous vacuole membrane (PVM), which implies that this protein may be involved in lipid remodelling in the PVM, or in the transport of fatty acids across the membrane.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Functional characterization of a fatty acyl-CoA-binding protein (ACBP) from the apicomplexan Cryptosporidium parvum

2006

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“…Plasmodium falciparum acylCoA-binding protein (ACBP, generously provided by Dr. Terry Smith, Dundee, Scotland, UK) was overexpressed in E. coli strain BL21DE3, using vector pET 16b-Plasmodium falciparum (PfACBP), and was purified to greater than 95% purity as judged by SDS-electrophoresis as described (39). ACBP was then directly coupled to a carboxymethylated dextran matrix (CM5 sensor chip, Biacore AB) through primary amine groups with a 1:1 mixture of N-ethyl-NЈ-(dimethylaminopropyl)-carbodiimide and N-hydroxysuccinimide according to the recommendations of the manufacturer (BIAcore AB).…”

Section: Construction Of Sbcad Prokaryotic Expression Vectors-mentioning

confidence: 99%

A Novel Approach to the Characterization of Substrate Specificity in Short/Branched Chain Acyl-CoA Dehydrogenase

Burghardt

Vockley

2003

Journal of Biological Chemistry

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Rat and human short/branched chain acyl-CoA dehydrogenases exhibit key differences in substrate specificity despite an overall amino acid identity of 85% between them. Rat short/branched chain acyl-CoA dehydrogenases (SBCAD) are more active toward substrates with longer carbon side chains than human SBCAD, whereas the human enzyme utilizes substrates with longer primary carbon chains. The mechanism underlying this difference in substrate specificity was investigated with a novel surface plasmon resonance assay combined with absorbance and circular dichroism spectroscopy, and kinetics analysis of wild type SBCADs and mutants with altered amino acid residues in the substrate binding pocket. Results show that a relatively few amino acid residues are critical for determining the difference in substrate specificity seen between the human and rat enzymes and that alteration of these residues influences different portions of the enzyme mechanism. Molecular modeling of the SBCAD structure suggests that position 104 at the bottom of the substrate binding pocket is important in determining the length of the primary carbon chain that can be accommodated. Conformational changes caused by alteration of residues at positions 105 and 177 directly affect the rate of electron transfer in the dehydrogenation reactions, and are likely transmitted from the bottom of the substrate binding pocket to ␤-sheet 3. Differences between the rat and human enzyme at positions 383, 222, and 220 alter substrate specificity without affecting substrate binding. Modeling predicts that these residues combine to determine the distance between the flavin ring of FAD and the catalytic base, without changing the opening of the substrate binding pocket.The acyl-CoA dehydrogenases (ACDs) 1 are a family of related enzymes that catalyze the ␣, ␤-dehydrogenation of acylCoA esters, transferring electrons to electron transferring flavoprotein (1-4). Deficiencies of these enzymes are important causes of human disease (3-7). Biochemical and immunological studies have identified at least 9 distinct members of this enzyme family, each having a characteristic substrate utilization pattern (8 -13). Very long, long, medium, and short chain acyl-CoA dehydrogenases (VLCAD, LCAD, MCAD, and SCAD, respectively) catalyze the first step in the mitochondrial ␤-oxidation of fatty acids with substrate optima of 16, 16, 8, and 4 carbon chains, respectively (3, 14 -15). A new ACD has been identified recently (ACAD9) that is also active against long chain acyl-CoA substrates (16). Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenase (SBCAD, also known as 2-methyl branched chain acyl-CoA dehydrogenase), and isobutyryl-CoA dehydrogenase (IBD) catalyze the third step in leucine, isoleucine, and valine metabolism, respectively (2-4, 11, 12, 17, 18), whereas glutaryl-CoA dehydrogenase is active in lysine metabolism (19).We have shown previously that SCAD, SBCAD, and IBD can all utilize butyryl-CoA as substrate (albeit with different efficiencies), whereas ...

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“…Comparison of bovine, insect and yeast ACBPs shows a nearly identical architecture of helical elements with conformational variation in the connecting loops. This variation might be related to binding specificity, affinity for different ligands (van Aalten et al, 2001) and crystallographic contacts (see below), as well as to differential interaction with membranes and macromolecules (Vallejo, 2006). The loop between helix 1 and 2, at the rim of the binding site, is of particular interest because it exhibits significant changes in length and sequence among animal, yeast and insect ACBPs and may be related to species differences in ligand selectivity (van Aalten et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

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

Costabel

Ermácora

Santomé

et al. 2006

Acta Crystallogr F Struct Biol Cryst Commun

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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.

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Binding site differences revealed by crystal structures of Plasmodium falciparum and bovine acyl-CoA binding protein

Cited by 59 publications

References 27 publications

Functional characterization of a fatty acyl-CoA-binding protein (ACBP) from the apicomplexan Cryptosporidium parvum

Functional characterization of a fatty acyl-CoA-binding protein (ACBP) from the apicomplexan Cryptosporidium parvum

A Novel Approach to the Characterization of Substrate Specificity in Short/Branched Chain Acyl-CoA Dehydrogenase

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

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