Summary: Prokaryotic acetaldehyde dehydrogenase, dimerisation
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This is the Wikipedia entry entitled "Prokaryotic acetaldehyde dehydrogenase dimerisation domain". More...
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Prokaryotic acetaldehyde dehydrogenase dimerisation domain Edit Wikipedia article
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crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate
In molecular biology, prokaryotic acetaldehyde dehydrogenase dimerisation domain is a protein domain found at the C-terminus of prokaryotic acetaldehyde dehydrogenases, it adopts a structure consisting of an alpha-beta-alpha-beta(3) core, which mediates dimerisation of the protein.
The acetaldehyde dehydrogenase family of bacterial enzymes catalyses the formation of acetyl-CoA from acetaldehyde in the 3-hydroxyphenylpropinoate degradation pathway. It occurs as a late step in the meta-cleavage pathways of a variety of compounds, including catechol, biphenyl, toluene, salicylate.
- Manjasetty BA, Powlowski J, Vrielink A (June 2003). "Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate". Proc. Natl. Acad. Sci. U.S.A. 100 (12): 6992–7. doi:10.1073/pnas.1236794100. PMC . PMID 12764229.
- Shingler V, Powlowski J, Marklund U (February 1992). "Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600". J. Bacteriol. 174 (3): 711–24. PMC . PMID 1732207.
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Prokaryotic acetaldehyde dehydrogenase, dimerisation Provide feedback
Members of this family are found in prokaryotic acetaldehyde dehydrogenase (acylating), and adopt a structure consisting of an alpha-beta-alpha-beta(3) core. They mediate dimerisation of the protein .
Manjasetty BA, Powlowski J, Vrielink A; , Proc Natl Acad Sci U S A 2003;100:6992-6997.: Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. PUBMED:12764229 EPMC:12764229
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015426
This C-terminal domain is found in prokaryotic acetaldehyde dehydrogenases, it adopts a structure consisting of an alpha-beta-alpha-beta(3) core, which mediates dimerisation of the protein [ PUBMED:12764229 ].
The acetaldehyde dehydrogenase family of bacterial enzymes catalyses the formation of acetyl-CoA from acetaldehyde in the 3-hydroxyphenylpropinoate degradation pathway. It occurs as a late step in the meta-cleavage pathways of a variety of compounds, including catechol, biphenyl, toluene, salicylate [ PUBMED:1732207 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||acetaldehyde dehydrogenase (acetylating) activity (GO:0008774)|
|Biological process||aromatic compound catabolic process (GO:0019439)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This clan contains the C terminal domains of dehydrogenase enzymes involved in the biosynthesis of arginine, aspartate and aspartate derived amino acids. It also contains the C terminal domain of GAPDH, a dehydrogenase involved in glycolysis and gluconeogenesis.
The clan contains the following 18 members:AcetDehyd-dimer Asp_DH_C Biliv-reduc_cat DapB_C DAPDH_C DXP_redisom_C G6PD_C GFO_IDH_MocA_C GFO_IDH_MocA_C2 Gp_dh_C Homoserine_dh Inos-1-P_synth OpcA_G6PD_C ox_reductase_C Oxidoreduct_C OxRdtase_C Sacchrp_dh_C Semialdhyde_dhC
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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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|Number in seed:||90|
|Number in full:||1685|
|Average length of the domain:||146.00 aa|
|Average identity of full alignment:||60 %|
|Average coverage of the sequence by the domain:||47.98 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
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How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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 AcetDehyd-dimer domain has been found. There are 9 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
|Protein||Predicted structure||External Information|
|P77580||View 3D Structure||Click here|
|P9WQH3||View 3D Structure||Click here|