Summary: Acyl-CoA dehydrogenase, middle domain
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Acyl-CoA dehydrogenase, middle domain Provide feedback
Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold.
Literature references
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Djordjevic S, Pace CP, Stankovich MT, Kim JJ; , Biochemistry. 1995;34:2163-2171.: Three-dimensional structure of butyryl-CoA dehydrogenase from Megasphaera elsdenii. PUBMED:7857927 EPMC:7857927
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Kim JJ, Wang M, Paschke R; , Proc Natl Acad Sci U S A 1993;90:7523-7527.: Crystal structures of medium-chain acyl-CoA dehydrogenase from pig liver mitochondria with and without substrate. PUBMED:8356049 EPMC:8356049
Internal database links
SCOOP: | HpaB_N |
Similarity to PfamA using HHSearch: | HpaB_N |
External database links
PROSITE: | PDOC00070 |
SCOP: | 1buc |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006091
Acyl-CoA dehydrogenases (EC) are a family of flavoproteins that catalyse the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with the concomitant reduction of enzyme-bound FAD. Different family members share a high sequence identity, catalytic mechanisms, and structural properties, but differ in the position of their catalytic bases and in their substrate binding specificity. Butyryl-CoA dehydrogenase [PUBMED:11812788] prefers short chain substrates, medium chain- and long-chain acyl-CoA dehydrogenases prefer medium and long chain substrates, respectively, and Isovaleryl-CoA dehydrogenase [PUBMED:9214289] prefers branched-chain substrates.
The monomeric enzyme is folded into three domains of approximately equal size, where the N-terminal domain is all-alpha, the middle domain is an open (5,8) barrel, and the C-terminal domain is a four-helical bundle. The constituent families differ in the numbers of C-terminal domains. This entry represents the middle beta-barrel domain found in medium chain acyl-CoA dehydrogenases, as well as in the related peroxisomal acyl-CoA oxidase-II enzymes. Acyl-CoA oxidase (ACO; EC) catalyzes the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids [PUBMED:11872165].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627) |
Biological process | oxidation-reduction process (GO:0055114) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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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 (41) |
Full (71135) |
Representative proteomes | UniProt (289767) |
NCBI (396410) |
Meta (8835) |
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RP15 (7319) |
RP35 (28430) |
RP55 (68596) |
RP75 (125814) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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Seed (41) |
Full (71135) |
Representative proteomes | UniProt (289767) |
NCBI (396410) |
Meta (8835) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (7319) |
RP35 (28430) |
RP55 (68596) |
RP75 (125814) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
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.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Prosite |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 41 |
Number in full: | 71135 |
Average length of the domain: | 98.80 aa |
Average identity of full alignment: | 29 % |
Average coverage of the sequence by the domain: | 21.43 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 97 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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Interactions
There are 8 interactions for this family. More...
ETF_alpha Acyl-CoA_dh_1 Acyl-CoA_dh_M Acyl-CoA_ox_N ACOX Acyl-CoA_dh_1 Acyl-CoA_dh_N ACOXStructures
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 Acyl-CoA_dh_M domain has been found. There are 370 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 sequence.
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