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.
30  structures 5229  species 2  interactions 11443  sequences 45  architectures

Family: CTDII (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

DnaJ domain
PBB Protein DNAJB1 image.jpg
PDB rendering based on 1hdj.
Identifiers
Symbol DnaJ
Pfam PF00226
InterPro IPR001623
PROSITE PDOC00553
SCOP 1xbl
SUPERFAMILY 1xbl
CDD cd06257
DnaJ central domain
Identifiers
Symbol DnaJ_CXXCXGXG
Pfam PF00684
Pfam clan CL0518
InterPro IPR001305
PROSITE PDOC00553
SCOP 1exk
SUPERFAMILY 1exk
DnaJ C terminal domain
PDB 1nlt EBI.jpg
the crystal structure of hsp40 ydj1
Identifiers
Symbol DnaJ_C
Pfam PF01556
InterPro IPR002939
PROSITE PDOC00553
SCOP 1exk
SUPERFAMILY 1exk

In molecular biology, chaperone DnaJ, also known as Hsp40 (heat shock protein 40 kD), is a molecular chaperone protein. It is expressed in a wide variety of organisms from bacteria to humans.[1][2]

Function

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-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.[3] 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.[4] DnaJ heat-shock proteins play a role in regulating the ATPase activity of Hsp70 heat-shock proteins.[5][6]

Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation.[7] 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.

Domain architecture

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. [8] The function of the C-terminal is chaperone and dimerization.

Human proteins containing a DnaJ domain

DNAJA1; DNAJA2; DNAJA3; DNAJA4; DNAJB1; DNAJB11; DNAJB13; DNAJB4; DNAJB5; DNAJC17; MST104;

References

  1. ^ 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 : CMLS 63 (22): 2560–70. doi:10.1007/s00018-006-6192-6. PMID 16952052. 
  2. ^ 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): 555–63. doi:10.1091/mbc.4.6.555. PMC 300962. PMID 8374166. 
  3. ^ Douglas MG, Cyr DM, Langer T (1994). "DnaJ-like proteins: molecular chaperones and specific regulators of Hsp70". Trends Biochem. Sci. 19 (4): 176–181. doi:10.1016/0968-0004(94)90281-x. PMID 8016869. 
  4. ^ 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 : a publication of the Protein Society 14 (7): 1697–709. doi:10.1110/ps.051406805. PMC 2253343. PMID 15987899. 
  5. ^ Fan CY, Lee S, Cyr DM (2003). "Mechanisms for regulation of Hsp70 function by Hsp40". Cell stress & chaperones 8 (4): 309–16. doi:10.1379/1466-1268(2003)008<0309:MFROHF>2.0.CO;2. PMC 514902. PMID 15115283. 
  6. ^ Ohtsuka K, Hata M (2000). "Molecular chaperone function of mammalian Hsp70 and Hsp40--a review". International journal of hyperthermia : the official journal of European Society for Hyperthermic Oncology, North American Hyperthermia Group 16 (3): 231–45. doi:10.1080/026567300285259. PMID 10830586. 
  7. ^ Christen P, Han W (2004). "cis-Effect of DnaJ on DnaK in ternary complexes with chimeric DnaK/DnaJ-binding peptides". FEBS Lett. 563 (1): 146–150. doi:10.1016/S0014-5793(04)00290-X. PMID 15063739. 
  8. ^ 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 DnaJ☆☆☆". Journal of Molecular Biology 300 (4): 805–818. doi:10.1006/jmbi.2000.3923. PMID 10891270.  edit

This article incorporates text from the public domain Pfam and InterPro IPR002939

This article incorporates text from the public domain Pfam and InterPro IPR001623

This article incorporates text from the public domain Pfam and InterPro IPR001305

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 form 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 this, CTDII, are necessary for maintaining the J-domains in their specific relative positions [2].

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


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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 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
(113)
Full
(11443)
Representative proteomes NCBI
(8830)
Meta
(3406)
RP15
(1220)
RP35
(2251)
RP55
(3021)
RP75
(3594)
Jalview View  View  View  View  View  View  View  View 
HTML View    View  View  View  View     
PP/heatmap 1   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
(113)
Full
(11443)
Representative proteomes NCBI
(8830)
Meta
(3406)
RP15
(1220)
RP35
(2251)
RP55
(3021)
RP75
(3594)
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
(113)
Full
(11443)
Representative proteomes NCBI
(8830)
Meta
(3406)
RP15
(1220)
RP35
(2251)
RP55
(3021)
RP75
(3594)
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_342 (release 4.0)
Previous IDs: DnaJ_C;
Type: Domain
Author: Bashton M, Bateman A
Number in seed: 113
Number in full: 11443
Average length of the domain: 77.70 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 24.15 %

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 30.5 30.5
Trusted cut-off 30.5 30.5
Noise cut-off 30.4 30.4
Model length: 81
Family (HMM) version: 13
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 2 interactions for this family. More...

CTDII DnaJ_CXXCXGXG

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 CTDII domain has been found. There are 30 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...