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.
36  structures 9222  species 1  interaction 22054  sequences 165  architectures

Family: DnaJ_C (PF01556)

Summary: DnaJ C terminal domain

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 "Chaperone DnaJ". More...

Chaperone DnaJ Edit Wikipedia article

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.

DnaJ C terminal domain Provide feedback

This family consists of the C terminal region of the DnaJ protein. It is always found associated with PF00226 and PF00684. DnaJ is a chaperone associated with the Hsp70 heat-shock system involved in protein folding and renaturation after stress. The two C-terminal domains CTDI and CTDII, both incorporated in this family are necessary for maintaining the J-domains in their specific relative positions [2]. Structural analysis of PDB:1nlt shows that PF00684 is nested within this DnaJ C-terminal region [3].

Literature references

  1. Kelley WL; , Trends Biochem Sci 1998;23:222-227.: The J-domain family and the recruitment of chaperone power. PUBMED:9644977 EPMC:9644977

  2. Silva JC, Borges JC, Cyr DM, Ramos CH, Torriani IL;, BMC Struct Biol. 2011;11:40.: Central domain deletions affect the SAXS solution structure and function of yeast Hsp40 proteins Sis1 and Ydj1. PUBMED:22011374 EPMC:22011374

  3. Li J, Qian X, Sha B;, Structure. 2003;11:1475-1483.: The crystal structure of the yeast Hsp40 Ydj1 complexed with its peptide substrate. PUBMED:14656432 EPMC:14656432


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002939

Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold [PUBMED:8016869]. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.

Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation [PUBMED:15063739]. Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate.

This domain consists of the C-terminal region of the DnaJ protein. The function of this domain is unknown. It is found associated with INTERPRO and INTERPRO. DnaJ is a chaperone associated with the Hsp70 heat-shock system involved in protein folding and renaturation after stress. The two C-terminal domains CTDI and this, CTDII, are necessary for maintaining the J-domains in their specific relative positions [PUBMED:22011374].

Domain organisation

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

Loading domain graphics...

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 (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...

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
(1171)
Full
(22054)
Representative proteomes UniProt
(51696)
NCBI
(58820)
Meta
(3769)
RP15
(5753)
RP35
(13528)
RP55
(19776)
RP75
(26470)
Jalview View  View  View  View  View  View  View  View  View 
HTML View                 
PP/heatmap 1                

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

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

Format an alignment

  Seed
(1171)
Full
(22054)
Representative proteomes UniProt
(51696)
NCBI
(58820)
Meta
(3769)
RP15
(5753)
RP35
(13528)
RP55
(19776)
RP75
(26470)
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
(1171)
Full
(22054)
Representative proteomes UniProt
(51696)
NCBI
(58820)
Meta
(3769)
RP15
(5753)
RP35
(13528)
RP55
(19776)
RP75
(26470)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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_342 (release 4.0)
Previous IDs: DnaJ_C; CTDII;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bashton M , Bateman A
Number in seed: 1171
Number in full: 22054
Average length of the domain: 193.50 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 51.71 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.6 26.6
Trusted cut-off 26.6 26.6
Noise cut-off 26.3 26.5
Model length: 148
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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 is 1 interaction for this family. More...

DnaJ_C

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 DnaJ_C domain has been found. There are 36 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.

Loading structure mapping...