Summary: VDE lipocalin domain
VDE lipocalin domain Provide feedback
This family represents a conserved region approximately 150 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage .
Bugos RC, Yamamoto HY; , Proc Natl Acad Sci U S A 1996;93:6320-6325.: Molecular cloning of violaxanthin de-epoxidase from romaine lettuce and expression in Escherichia coli. PUBMED:8692813 EPMC:8692813
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR010788
This family represents a conserved region approximately 350 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage [PUBMED:8692813].
|Cellular component||chloroplast (GO:0009507)|
|Molecular function||violaxanthin de-epoxidase activity (GO:0046422)|
|Biological process||oxidation-reduction process (GO:0055114)|
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This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
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The calycin structural superfamily [1-3] includes the lipocalins, the fatty acid-binding proteins (FABPs).
The clan contains the following 20 members:ApoM CrtC DUF3642 DUF4488 DUF4822 His_binding Lipocalin Lipocalin_2 Lipocalin_3 Lipocalin_4 Lipocalin_5 Lipocalin_7 Lipocalin_8 META Nitrophorin NlpE Svf1 Triabin VDE ZinT
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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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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Curation and family details
|Seed source:||Pfam-B_12679 (release 10.0)|
|Author:||Vella Briffa B|
|Number in seed:||2|
|Number in full:||158|
|Average length of the domain:||177.60 aa|
|Average identity of full alignment:||56 %|
|Average coverage of the sequence by the domain:||48.51 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 VDE domain has been found. There are 4 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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