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3  structures 3093  species 0  interactions 5528  sequences 57  architectures

Family: DnaJ_CXXCXGXG (PF00684)

Summary: DnaJ central domain

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DnaJ central domain Provide feedback

The central cysteine-rich (CR) domain of DnaJ proteins 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 [1].

Literature references

  1. Martinez-Yamout M, Legge GB, Zhang O, Wright PE, Dyson HJ; , J Mol Biol 2000;300:805-818.: Solution Structure of the Cysteine-rich Domain of the Escherichia coli Chaperone Protein DnaJ. PUBMED:10891270 EPMC:10891270

  2. 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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001305

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]. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation [PUBMED:15063739].

DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) [PUBMED:15170475].

This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and 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 [PUBMED:10891270].

Gene Ontology

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Domain organisation

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

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Alignments

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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
(1550)
Full
(5528)
Representative proteomes UniProt
(17646)
NCBI
(19902)
Meta
(2174)
RP15
(1398)
RP35
(3500)
RP55
(5625)
RP75
(8121)
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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
(1550)
Full
(5528)
Representative proteomes UniProt
(17646)
NCBI
(19902)
Meta
(2174)
RP15
(1398)
RP35
(3500)
RP55
(5625)
RP75
(8121)
Alignment:
Format:
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Sequence:
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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
(1550)
Full
(5528)
Representative proteomes UniProt
(17646)
NCBI
(19902)
Meta
(2174)
RP15
(1398)
RP35
(3500)
RP55
(5625)
RP75
(8121)
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.

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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_89 (release 2.1)
Previous IDs: none
Type: Domain
Author: Yamout M, Bateman A
Number in seed: 1550
Number in full: 5528
Average length of the domain: 64.40 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 15.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 32.7 32.7
Trusted cut-off 32.7 32.7
Noise cut-off 32.6 32.6
Model length: 67
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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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_CXXCXGXG domain has been found. There are 3 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.

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