The hsp70 chaperone machine (see <PDOC00269>) 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 [1,2].

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) [2].

Such a structure is shown in the following schematic representation:

    +------------+-+-----------+-----+-----------+-------------+
    |  J-domain  | | Gly/Phe-R |     | CXXCXGXG  |     CTD     |
    +------------+-+-----------+-----+-----------+-------------+

The structures of the 'J' domain (see <PDB:1XBL>) and the 'CR' domain (see <PDB:1EXK>) have been solved [3,4]. 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 [5]. The CR-type zinc finger has an overall V-shaped extended β-hairpin topology and two symmetrical zinc binding sites, designated as Zn1 and Zn2: Zn1 is formed by the two cysteine motifs that are furthest apart in the primary sequence, while Zn2 is formed by the two central, adjacent cysteine motifs [4]. It has been shown that Zn1 is important for the autonomous, dnaK-independent chaperone activity, while Zn2 is a necessary interaction site with dnaK, which seems to be crucial for in vivo function in the dnaJ/dnaK system [6].

J-protein family are classified in three classes [2]:

The type 1 contains proteins with a J-domain, a G/F domain, a CR zinc finger and a CTD domain (true homologues of dnaJ):

• Yeast protein MAS5/YDJ1 that is involved in protein folding and mitochondrial protein import.
• Yeast protein MDJ1 that is involved in protein folding and mitochondrial protein import.
• Yeast protein SCJ1 that is involved in protein folding in the lumen of the endoplasmic reticulum.
• Yeast protein APJ1/YNL077w, that might modulate folding reaction.
• Cucumber dnaJ homolog anchored at the glyoxysomal membrane.
• Yeast protein XDJ1.
• Human protein HDJ2.

The type 2 contains proteins with a J-domain, a G/F domain and a CTD domain:

• Rhizobium fredii nolC, a protein involved in cultivar-specific nodulation of soybean.
• Escherichia coli cbpA, a protein that binds curved DNA.
• Yeast protein SIS1, required for nuclear migration during mitosis.
• Yeast protein CAJ1.
• Yeast hypothetical protein YFR041c.
• Yeast hypothetical protein YIR004w.
• Yeast hypothetical protein YJL162c.
• Plasmodium falciparum ring-infected erythrocyte surface antigen (RESA). RESA, whose function is not known, is associated with the membrane skeleton of newly invaded erythrocytes.
• Human HDJ1.
• Human HSJ1, a neuronal protein.
• Drosophila cysteine-string protein (csp).

The type 3 subgroup contains proteins that have only the J-domain:

• Yeast protein SEC63/NPL1. It is important for protein assembly into the endoplasmic reticulum and the nucleus.
• Eukaryotic Tim14 protein. An essential component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. In the complex, it is required to stimulate activity of mtHSP70 (SSC1).
• Yeast Jac1 protein and HscB eukaryotic homologues. They may act as co-chaperones in iron-sulfur cluster assembly in mitochondria.
• Yeast Zuo1 protein. Zuo1 and Ssz1 (hsp70) are targeted to ribosomes, where they form the functionally active RAC complex.
• Yeast Jjj1 to 3, Erj5 and Jid1 proteins of unknown function.

We developed a signature pattern for the 'J' domain, based on conserved positions in the C-terminal half of this domain. We also developed two profiles, one which covers the entire 'J' domain and the other that spans the whole CR-type zinc finger.