Summary: Cell division protein 48 (CDC48), N-terminal domain
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This is the Wikipedia entry entitled "CDC48 N-terminal domain". More...
CDC48 N-terminal domain Edit Wikipedia article
CDC48_N | |||||||||
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![]() crystal structure of aaa atpase p97/vcp nd1 in complex with p47 c
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Identifiers | |||||||||
Symbol | CDC48_N | ||||||||
Pfam | PF02359 | ||||||||
InterPro | IPR003338 | ||||||||
SCOP | 1cz4 | ||||||||
SUPERFAMILY | 1cz4 | ||||||||
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CDC48_2 | |||||||||
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![]() amino terminal domain of the n-ethylmaleimide sensitive fusion protein (nsf)
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Identifiers | |||||||||
Symbol | CDC48_2 | ||||||||
Pfam | PF02933 | ||||||||
Pfam clan | CL0402 | ||||||||
InterPro | IPR004201 | ||||||||
SCOP | 1cz4 | ||||||||
SUPERFAMILY | 1cz4 | ||||||||
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In molecular biology, the CDC48 N-terminal domain is a protein domain found in AAA ATPases including cell division protein 48 (CDC48), VCP-like ATPase and N-ethylmaleimide sensitive fusion protein. It is a substrate recognition domain which binds polypeptides, prevents protein aggregation, and catalyses refolding of permissive substrates. It is composed of two equally sized subdomains. The amino-terminal subdomain (CDC48_N) forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain (CDC48_2) forms a novel six-stranded beta-clam fold.[1] Together these subdomains form a kidney-shaped structure, in close agreement with results from electron microscopy. CDC48_N is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases.
References
- ^ Coles M, Diercks T, Liermann J, Groger A, Rockel B, Baumeister W, Koretke KK, Lupas A, Peters J, Kessler H (October 1999). "The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element". Curr. Biol. 9 (20): 1158–68. doi:10.1016/S0960-9822(00)80017-2. PMID 10531028.
This article incorporates text from the public domain Pfam and InterPro IPR003338
This article incorporates text from the public domain Pfam and InterPro IPR004201
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Cell division protein 48 (CDC48), N-terminal domain Provide feedback
This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases PF00004 is a substrate 185-residue recognition domain [1].
Literature references
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Coles M, Diercks T, Liermann J, Groger A, Rockel B, Baumeister W, Koretke KK, Lupas A, Peters J, Kessler H; , Curr Biol 1999;9:1158-1168.: The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element. PUBMED:10531028 EPMC:10531028
Internal database links
SCOOP: | Molydop_binding UFD1 |
Similarity to PfamA using HHSearch: | Molydop_binding |
External database links
SCOP: | 1cz4 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR003338
The CDC48 N-terminal domain is a protein domain found in AAA ATPases including cell division protein 48 (CDC48), VCP-like ATPase (VAT) and N-ethylmaleimide sensitive fusion protein. It is a substrate recognition domain which binds polypeptides, prevents protein aggregation, and catalyses refolding of permissive substrates. It is composed of two equally sized subdomains. The amino-terminal subdomain forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain forms a novel six-stranded beta-clam fold [PUBMED:10531028]. Together these subdomains form a kidney-shaped structure.
This entry represents the amino-terminal subdomain.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan AcetylDC-like (CL0332), which has the following description:
These families are double psi-beta barrel structures.
The clan contains the following 4 members:
Asp_decarbox CDC48_N Molydop_binding PEX-2NAlignments
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 (99) |
Full (3417) |
Representative proteomes | UniProt (8649) |
NCBI (10314) |
Meta (109) |
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RP15 (473) |
RP35 (1438) |
RP55 (2838) |
RP75 (4336) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (99) |
Full (3417) |
Representative proteomes | UniProt (8649) |
NCBI (10314) |
Meta (109) |
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RP15 (473) |
RP35 (1438) |
RP55 (2838) |
RP75 (4336) |
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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.
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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: | Pfam-B_799 (release 5.2) |
Previous IDs: | VAT-Nn; cdc48_N; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bashton M |
Number in seed: | 99 |
Number in full: | 3417 |
Average length of the domain: | 83.30 aa |
Average identity of full alignment: | 34 % |
Average coverage of the sequence by the domain: | 10.95 % |
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: | 85 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 CDC48_N domain has been found. There are 218 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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