Summary: DnaJ domain
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This is the Wikipedia entry entitled "Chaperone DnaJ". More...
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Chaperone DnaJ Edit Wikipedia article
|SCOP2||1xbl / SCOPe / SUPFAM|
|DnaJ central domain|
|SCOP2||1exk / SCOPe / SUPFAM|
|DnaJ C terminal domain|
|SCOP2||1exk / SCOPe / SUPFAM|
Molecular chaperones are a diverse family of proteins that function to protect proteins 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-hydrolyzing 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. 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.
This family of proteins contain a 70 amino acid consensus sequence known as the J domain. The J domain of DnaJ interacts with Hsp70 heat shock proteins. DnaJ heat-shock proteins play a role in regulating the ATPase activity of Hsp70 heat-shock proteins.
Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation. 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.
Proteins in this family consist of three domains. The N-terminal domain is the J domain (described above). The central domain is a cysteine-rich region, which contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DNAJ cysteine rich domain and various hydrophobic peptides has been found. This domain has disulphide isomerase activity. The function of the C-terminal is chaperone and dimerization.
Proteins containing a DnaJ domain
- Homo sapiens: DNAJA1; DNAJA2; DNAJA3; DNAJA4 (MST104); DNAJB1; DNAJB11; DNAJB13; DNAJB4; DNAJB5; DNAJB6; DNAJC17; DNAJC28
- Saccharomyces cerevisiae: ZUO1
- Qiu XB, Shao YM, Miao S, Wang L (November 2006). "The diversity of the DnaJ/Hsp40 family, the crucial partners for Hsp70 chaperones". Cellular and Molecular Life Sciences. 63 (22): 2560â€“70. doi:10.1007/s00018-006-6192-6. PMIDÂ 16952052. S2CIDÂ 21325339.
- Caplan AJ, Cyr DM, Douglas MG (June 1993). "Eukaryotic homologues of Escherichia coli dnaJ: a diverse protein family that functions with hsp70 stress proteins". Molecular Biology of the Cell. 4 (6): 555â€“63. doi:10.1091/mbc.4.6.555. PMCÂ 300962. PMIDÂ 8374166.
- Douglas MG, Cyr DM, Langer T (1994). "DnaJ-like proteins: molecular chaperones and specific regulators of Hsp70". Trends Biochem. Sci. 19 (4): 176â€“181. doi:10.1016/0968-0004(94)90281-x. PMIDÂ 8016869.
- Hennessy F, Nicoll WS, Zimmermann R, Cheetham ME, Blatch GL (July 2005). "Not all J domains are created equal: implications for the specificity of Hsp40-Hsp70 interactions". Protein Science. 14 (7): 1697â€“709. doi:10.1110/ps.051406805. PMCÂ 2253343. PMIDÂ 15987899.
- Fan CY, Lee S, Cyr DM (2003). "Mechanisms for regulation of Hsp70 function by Hsp40". Cell Stress & Chaperones. 8 (4): 309â€“16. doi:10.1379/1466-1268(2003)008<0309:MFROHF>2.0.CO;2. PMCÂ 514902. PMIDÂ 15115283.
- Ohtsuka K, Hata M (2000). "Molecular chaperone function of mammalian Hsp70 and Hsp40--a review". International Journal of Hyperthermia. 16 (3): 231â€“45. doi:10.1080/026567300285259. PMIDÂ 10830586. S2CIDÂ 22622220.
- Christen P, Han W (2004). "cis-Effect of DnaJ on DnaK in ternary complexes with chimeric DnaK/DnaJ-binding peptides". FEBS Lett. 563 (1): 146â€“150. doi:10.1016/S0014-5793(04)00290-X. PMIDÂ 15063739. S2CIDÂ 11050399.
- Martinez-Yamout, M.; Legge, G. B.; Zhang, O.; Wright, P. E.; Dyson, H. J. (2000). "Solution Structure of the Cysteine-rich Domain of the Escherichia coli Chaperone Protein DnaJâ˜†â˜†â˜†". Journal of Molecular Biology. 300 (4): 805â€“818. doi:10.1006/jmbi.2000.3923. PMIDÂ 10891270.
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 domain Provide feedback
DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are confirmed as DnaJ containing domains from literature .
Stubdal H, Zalvide J, Campbell KS, Schweitzer C, Roberts TM, DeCaprio JA; , Mol Cell Biol 1997;17:4979-4990.: Inactivation of pRB-related proteins p130 and p107 mediated by the J domain of simian virus 40 large T antigen. PUBMED:9271376 EPMC:9271376
Pellecchia M, Szyperski T, Wall D, Georgopoulos C, Wuthrich K; , J Mol Biol 1996;260:236-250.: NMR structure of the J-domain and the Gly/Phe-rich region of the Escherichia coli DnaJ chaperone. PUBMED:8764403 EPMC:8764403
Internal database links
|SCOOP:||DnaJ_C DUF87 Fer4_7 Pam16 RPT|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001623
The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to dnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of dnaK, which interacts stably with the polypeptide substrate [ PUBMED:11395418 , PUBMED:15170475 ].
Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues.
Such a structure is shown in the following schematic representation:
+------------+-+-------+-----+-----------+--------------------------------+ | J-domain | | Gly-R | | CXXCXGXG | C-terminal | +------------+-+-------+-----+-----------+--------------------------------+
The structure of the J-domain has been solved [ PUBMED:8764403 ]. The J domain consists of four helices, the second of which has a charged surface that includes basic residues that are essential for interaction with the ATPase domain of hsp70 [ PUBMED:12454054 ].
J-domains are found in many prokaryotic and eukaryotic proteins [ PUBMED:1585456 ]. In yeast, three J-like proteins have been identified containing regions closely resembling a J-domain, but lacking the conserved HPD motif - these proteins do not appear to act as molecular chaperones [ PUBMED:15170475 ].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
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Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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The J-domain is found in a number of stress-response proteins. It is found at the N-terminal of Hsc20, DnaJ-chaperone in E. coli, and viral large T-antigen proteins; it is also in Hsc40, mammalian auxilin and in both animal and plant DnaJ proteins. It is also found in degenerate form in Pam16 proteins.
The clan contains the following 2 members:DnaJ Pam16
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
|Author:||Birney E , Finn RD|
|Number in seed:||222|
|Number in full:||92755|
|Average length of the domain:||62.50 aa|
|Average identity of full alignment:||37 %|
|Average coverage of the sequence by the domain:||15.03 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||34|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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 domain has been found. There are 97 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.