Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
49  structures 512  species 3  interactions 1049  sequences 16  architectures

Family: CDC48_2 (PF02933)

Summary: Cell division protein 48 (CDC48), domain 2

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "CDC48 N-terminal domain". More...

CDC48 N-terminal domain Edit Wikipedia article

CDC48_N
PDB 1s3s EBI.jpg
crystal structure of aaa atpase p97/vcp nd1 in complex with p47 c
Identifiers
Symbol CDC48_N
Pfam PF02359
InterPro IPR003338
SCOP 1cz4
SUPERFAMILY 1cz4
CDC48_2
PDB 1qdn EBI.jpg
amino terminal domain of the n-ethylmaleimide sensitive fusion protein (nsf)
Identifiers
Symbol CDC48_2
Pfam PF02933
Pfam clan CL0402
InterPro IPR004201
SCOP 1cz4
SUPERFAMILY 1cz4

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[edit]

  1. ^ 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), domain 2 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 C-terminus. The VAT-N domain found in AAA ATPases PF00004 is a substrate 185-residue recognition domain [1].

Literature references

  1. 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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004201

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 carboxy-terminal subdomain.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan Cdc48_2-like (CL0402), which has the following description:

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

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(103)
Full
(1049)
Representative proteomes NCBI
(1072)
Meta
(104)
RP15
(197)
RP35
(383)
RP55
(563)
RP75
(687)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(103)
Full
(1049)
Representative proteomes NCBI
(1072)
Meta
(104)
RP15
(197)
RP35
(383)
RP55
(563)
RP75
(687)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(103)
Full
(1049)
Representative proteomes NCBI
(1072)
Meta
(104)
RP15
(197)
RP35
(383)
RP55
(563)
RP75
(687)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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 View help on the curation process

Seed source: Pfam-B_799 (release 5.2)
Previous IDs: cdc48_2;
Type: Domain
Author: Bashton M, Bateman A, Griffiths-Jones SR
Number in seed: 103
Number in full: 1049
Average length of the domain: 68.70 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 9.07 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.4 22.6
Noise cut-off 22.3 22.2
Model length: 64
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 3 interactions for this family. More...

AAA CDC48_N UBX

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_2 domain has been found. There are 49 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.

Loading structure mapping...