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29  structures 583  species 1  interaction 1677  sequences 62  architectures

Family: ACBP (PF00887)

Summary: Acyl CoA binding protein

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This is the Wikipedia entry entitled "Acyl-CoA-binding protein". More...

Acyl-CoA-binding protein Edit Wikipedia article

ACBP
PDB 1hb8 EBI.jpg
structure of bovine acyl-coa binding protein in tetragonal crystal form
Identifiers
Symbol ACBP
Pfam PF00887
InterPro IPR000582
PROSITE PDOC00686
SCOP 1aca
SUPERFAMILY 1aca
CDD cd00435

In molecular biology, the Acyl-CoA-binding protein (ACBP) is a small (10 Kd) protein that binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters.[1] ACBP is also known as diazepam binding inhibitor (DBI) or endozepine (EP) because of its ability to displace diazepam from the benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore possible that this protein also acts as a neuropeptide to modulate the action of the GABA receptor.[2]

ACBP is a highly conserved protein of about 90 amino acids that is found in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and in some eubacterial species.[3]

Although ACBP occurs as a completely independent protein, intact ACB domains have been identified in a number of large, multifunctional proteins in a variety of eukaryotic species. These include large membrane-associated proteins with N-terminal ACB domains, multifunctional enzymes with both ACB and peroxisomal enoyl-CoA Delta(3), Delta(2)-enoyl-CoA isomerase domains, and proteins with both an ACB domain and ankyrin repeats.[3]

The ACB domain consists of four alpha-helices arranged in a bowl shape with a highly exposed acyl-CoA-binding site. The ligand is bound through specific interactions with residues on the protein, most notably several conserved positive charges that interact with the phosphate group on the adenosine-3'phosphate moiety, and the acyl chain is sandwiched between the hydrophobic surfaces of CoA and the protein.[4]

Other proteins containing an ACB domain include:

  • DRS-1,[6] a human protein of unknown function that contains a N-terminal ACB domain and a C-terminal enoyl-CoA isomerase/hydratase domain.

References[edit]

  1. ^ Rose TM, Schultz ER, Todaro GJ (December 1992). "Molecular cloning of the gene for the yeast homolog (ACB) of diazepam binding inhibitor/endozepine/acyl-CoA-binding protein". Proc. Natl. Acad. Sci. U.S.A. 89 (23): 11287–91. doi:10.1073/pnas.89.23.11287. PMC 50535. PMID 1454809. 
  2. ^ Costa E, Guidotti A (1991). "Diazepam binding inhibitor (DBI): a peptide with multiple biological actions". Life Sci. 49 (5): 325–44. doi:10.1016/0024-3205(91)90440-M. PMID 1649940. 
  3. ^ a b Burton M, Rose TM, Faergeman NJ, Knudsen J (December 2005). "Evolution of the acyl-CoA binding protein (ACBP)". Biochem. J. 392 (Pt 2): 299–307. doi:10.1042/BJ20050664. PMC 1316265. PMID 16018771. 
  4. ^ van Aalten DM, Milne KG, Zou JY, Kleywegt GJ, Bergfors T, Ferguson MA, Knudsen J, Jones TA (May 2001). "Binding site differences revealed by crystal structures of Plasmodium falciparum and bovine acyl-CoA binding protein". J. Mol. Biol. 309 (1): 181–92. doi:10.1006/jmbi.2001.4749. PMID 11491287. 
  5. ^ Pusch W, Balvers M, Hunt N, Ivell R (August 1996). "A novel endozepine-like peptide (ELP) is exclusively expressed in male germ cells". Mol. Cell. Endocrinol. 122 (1): 69–80. doi:10.1016/0303-7207(96)03874-9. PMID 8898349. 
  6. ^ Suk K, Kim YH, Hwang DY, Ihm SH, Yoo HJ, Lee MS (May 1999). "Molecular cloning and expression of a novel human cDNA related to the diazepam binding inhibitor". Biochim. Biophys. Acta 1454 (1): 126–31. PMID 10354522. 

This article incorporates text from the public domain Pfam and InterPro IPR000582

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External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000582

Acyl-CoA-binding protein (ACBP) is a small (10 Kd) protein that binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters [PUBMED:1454809]. ACBP is also known as diazepam binding inhibitor (DBI) or endozepine (EP) because of its ability to displace diazepam from the benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore possible that this protein also acts as a neuropeptide to modulate the action of the GABA receptor [PUBMED:1649940].

ACBP is a highly conserved protein of about 90 residues that is found in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and in some eubacterial species [PUBMED:16018771].

Although ACBP occurs as a completely independent protein, intact ACB domains have been identified in a number of large, multifunctional proteins in a variety of eukaryotic species. These include large membrane-associated proteins with N-terminal ACB domains, multifunctional enzymes with both ACB and peroxisomal enoyl-CoA Delta(3), Delta(2)-enoyl-CoA isomerase domains, and proteins with both an ACB domain and ankyrin repeats (INTERPRO) [PUBMED:16018771].

The ACB domain consists of four alpha-helices arranged in a bowl shape with a highly exposed acyl-CoA-binding site. The ligand is bound through specific interactions with residues on the protein, most notably several conserved positive charges that interact with the phosphate group on the adenosine-3'phosphate moiety, and the acyl chain is sandwiched between the hydrophobic surfaces of CoA and the protein [PUBMED:11491287].

Other proteins containing an ACB domain include:

  • Endozepine-like peptide (ELP) (gene DBIL5) from mouse [PUBMED:8898349]. ELP is a testis-specific ACBP homologue that may be involved in the energy metabolism of the mature sperm.
  • MA-DBI, a transmembrane protein of unknown function which has been found in mammals. MA-DBI contains a N-terminal ACB domain.
  • DRS-1 [PUBMED:10354522], a human protein of unknown function that contains a N-terminal ACB domain and a C-terminal enoyl-CoA isomerase/hydratase domain.

Gene Ontology

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Domain organisation

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(101)
Full
(1677)
Representative proteomes NCBI
(1596)
Meta
(101)
RP15
(305)
RP35
(482)
RP55
(749)
RP75
(963)
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Format an alignment

  Seed
(101)
Full
(1677)
Representative proteomes NCBI
(1596)
Meta
(101)
RP15
(305)
RP35
(482)
RP55
(749)
RP75
(963)
Alignment:
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  Seed
(101)
Full
(1677)
Representative proteomes NCBI
(1596)
Meta
(101)
RP15
(305)
RP35
(482)
RP55
(749)
RP75
(963)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_864 (release 3.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 101
Number in full: 1677
Average length of the domain: 85.20 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 33.64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.9 21.9
Trusted cut-off 22.2 22.3
Noise cut-off 21.5 21.8
Model length: 87
Family (HMM) version: 14
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Species distribution

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Interactions

There is 1 interaction for this family. More...

ACBP

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the ACBP domain has been found. There are 29 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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