Summary: Peroxisome biogenesis factor 1, N-terminal
Peroxisome biogenesis factor 1, N-terminal Provide feedback
Members of this family adopt a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation .
Shiozawa K, Maita N, Tomii K, Seto A, Goda N, Akiyama Y, Shimizu T, Shirakawa M, Hiroaki H; , J Biol Chem. 2004;279:50060-50068.: Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain. PUBMED:15328346 EPMC:15328346
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015342
This domain adopts a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation [PUBMED:15328346].
|Cellular component||peroxisome (GO:0005777)|
|Molecular function||ATP binding (GO:0005524)|
|Biological process||peroxisome organization (GO:0007031)|
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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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Superfamily contains C-terminal domains of N-ethylmaleimide sensitive fusion proteins, VCP-like ATPases, membrane fusion ATPase p97 domain 2, peroxisome biogenesis factor 1 (PEX-1), domain 2, and ubiquitin fusion degradation protein UFD1 families.
The clan contains the following 3 members:CDC48_2 PEX-1N UFD1
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
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Number in seed:||32|
|Number in full:||271|
|Average length of the domain:||81.00 aa|
|Average identity of full alignment:||35 %|
|Average coverage of the sequence by the domain:||7.38 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||6|
|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 PEX-1N domain has been found. There are 1 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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