PDBsum entry: 1hdj

Molecular chaperone

PDB-id

1hdj

Contents

Description

Header details

Protein chain

* Residue conservation analysis

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PDB id:

1hdj

Name:

Molecular chaperone

Title:

Human hsp40 (hdj-1), nmr

Structure:

Human hsp40. Chain: a. Fragment: j-domain. Synonym: hdj-1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

UniProt:

P25685 (DNJB1_HUMAN)

Seq:

Struc:

Seq:

340 a.a.

Struc:

77 a.a.*

Key:		PfamA domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Resolution:

not givenÅ

NMR structure:

20 models

Authors:

Y.Q.Qian,D.Patel,F.-U.Hartl,D.J.Mccoll

Key ref:

Y.Q.Qian et al. (1996). Nuclear magnetic resonance solution structure of the human Hsp40 (HDJ-1) J-domain.. J Mol Biol, 260, 224-235. [PubMed id: 8764402] [DOI: 10.1006/jmbi.1996.0394]

Date:

09-May-96

Release date:

08-Nov-96

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Key reference

DOI no: 10.1006/jmbi.1996.0394 J Mol Biol 260:224-235 (1996)

PubMed id: 8764402

Nuclear magnetic resonance solution structure of the human Hsp40 (HDJ-1) J-domain.

Y.Q.Qian, D.Patel, F.U.Hartl, D.J.McColl.

ABSTRACT

The J-domain is a highly conserved domain found in all members of the DnaJ family of molecular chaperones. The three-dimensional structure of a recombinant, uniformly 15N-labeled 77-residue polypeptide containing the complete J-domain from human Hsp40 (HDJ-1) has been determined by nuclear magnetic resonance (NMR) spectroscopy in solution. On the basis of 876 upper distance constraints derived from nuclear Overhauser effects (NOE) and 173 dihedral angle constraints, a group of 20 conformers representing the solution structure of the HDJ-1 J-domain was computed with the program DIANA and energy-minimized with the program OPAL. The average of the pairwise root-mean-square deviations of the individual NMR conformers relative to the mean coordinates for the backbone atoms N, C2 and C' of residues 4 to 54 and 4 to to 66 is 0.88 and 0.99 A respectively. The molecular architecture includes four helices composed of residues 5 to 9, 15 to 28, 40 to 54 and 60 to 66. A turn composed of residues 10 to 14 links helices I and II, and a loop composed of residues 29 to 39 containing a highly conserved tripeptide HPD (residues 31 to 33) connects the antiparallel helices II and III. The tertiary fold formed by helix I-turn-helix II-loop-helix III forms a closed structural core; the less defined helix IV stands away from the core of the domain. The side-chains of the tripeptide HPD extend out from the core of the structure in the opposite direction from helix IV. The structure supports the hypothesis that the highly conserved tripeptide could play a key role in the interaction of Hsp40 with the molecular chaperone, Hsp70.

Selected figure(s)

Figure 4.
Figure 4. Stereo view of the polypeptide backbone atoms N, C a and C' for the 20 energy-refined DIANA conformers of the HDJ-1 J-domain. The superposition was taken for best fit of the backbone atoms N, C a and C' of residues 4 to 54. The color coding is: residues 0 to 3, 10 to 14, green; 4 to 9 (helix I), white; 15 to 28 (helix II), magenta; 40 to 54 (helix III), yellow; 60 to 66 (helix IV), orange; 29 to 39, 55 to 59 and 67 to 76, cyan. Figure 7.
Figure 7. Ribbon drawing of one energy refined DIANA conformer of the HDJ-1 J-domain (residues 0 to 76). The chain termini are identified by the letters N and C. Helices I to IV are shown in cyan, the loop and turns connecting the helices are shown in orange. The HPD tripeptide is indicated by the residues in red (His31), green (Pro32) and blue (Asp33). Six highly conserved residues (positions 19, 27, 44, 50, 51 and 54) involved in the stabilization of the structural core of the J-domain are indicated in yellow.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 260, 224-235) copyright 1996.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id Reference

19633874 V.B.V Rajan, and P.D'Silva (2009).
Arabidopsis thaliana J-class heat shock proteins: cellular stress sensors.

Funct Integr Genomics, 9, 433-446.

18702525 A.K.Füzéry, M.Tonelli, D.T.Ta, G.Cornilescu, L.E.Vickery, and J.L.Markley (2008).
Solution structure of the iron-sulfur cluster cochaperone HscB and its binding surface for the iron-sulfur assembly scaffold protein IscU.

Biochemistry, 47, 9394-9404.

18490186 M.Kosmaoglou, N.Schwarz, J.S.Bett, and M.E.Cheetham (2008).
Molecular chaperones and photoreceptor function.

Prog Retin Eye Res, 27, 434-449.

17420601 M.Sato, H.Yamahata, S.Watanabe, K.Nimura-Matsune, and H.Yoshikawa (2007).
Characterization of dnaJ multigene family in the cyanobacterium Synechococcus elongatus PCC 7942.

Biosci Biotechnol Biochem, 71, 1021-1027.

17239655 W.S.Nicoll, M.Botha, C.McNamara, M.Schlange, E.R.Pesce, A.Boshoff, M.H.Ludewig, R.Zimmermann, M.E.Cheetham, J.P.Chapple, and G.L.Blatch (2007).
Cytosolic and ER J-domains of mammalian and parasitic origin can functionally interact with DnaK.

Int J Biochem Cell Biol, 39, 736-751.

16973605 J.G.Bird, S.Sharma, S.C.Roshwalb, J.R.Hoskins, and S.Wickner (2006).
Functional analysis of CbpA, a DnaJ homolog and nucleoid-associated DNA-binding protein.

J Biol Chem, 281, 34349-34356.

15987899 F.Hennessy, W.S.Nicoll, R.Zimmermann, M.E.Cheetham, and G.L.Blatch (2005).
Not all J domains are created equal: implications for the specificity of Hsp40-Hsp70 interactions.

Protein Sci, 14, 1697-1709.

15661747 J.C.Borges, H.Fischer, A.F.Craievich, and C.H.Ramos (2005).
Low resolution structural study of two human HSP40 chaperones in solution. DJA1 from subfamily A and DJB4 from subfamily B have different quaternary structures.

J Biol Chem, 280, 13671-13681.

16014958 K.A.Whalen, R.de Jesus, J.A.Kean, and B.S.Schaffhausen (2005).
Genetic analysis of the polyomavirus DnaJ domain.

J Virol, 79, 9982-9990.

15806324 T.Yamamoto, Y.Mori, T.Ishibashi, Y.Uchiyama, T.Ueda, T.Ando, J.Hashimoto, S.Kimura, and K.Sakaguchi (2005).
Interaction between proliferating cell nuclear antigen (PCNA) and a DnaJ induced by DNA damage.

J Plant Res, 118, 91-97.

15849180 Y.Y.Shi, X.G.Hong, and C.C.Wang (2005).
The C-terminal (331-376) sequence of Escherichia coli DnaJ is essential for dimerization and chaperone activity: a small angle X-ray scattering study in solution.

J Biol Chem, 280, 22761-22768.

14657253 C.Y.Fan, S.Lee, H.Y.Ren, and D.M.Cyr (2004).
Exchangeable chaperone modules contribute to specification of type I and type II Hsp40 cellular function.

Mol Biol Cell, 15, 761-773.

15273304 J.M.Gruschus, L.E.Greene, E.Eisenberg, and J.A.Ferretti (2004).
Experimentally biased model structure of the Hsc70/auxilin complex: substrate transfer and interdomain structural change.

Protein Sci, 13, 2029-2044.

15170475 P.Walsh, D.Bursać, Y.C.Law, D.Cyr, and T.Lithgow (2004).
The J-protein family: modulating protein assembly, disassembly and translocation.

EMBO Rep, 5, 567-571.

15232009 Y.Zhang, and E.R.Zuiderweg (2004).
The 70-kDa heat shock protein chaperone nucleotide-binding domain in solution unveiled as a molecular machine that can reorient its functional subdomains.

Proc Natl Acad Sci U S A, 101, 10272-10277.

15115283 C.Y.Fan, S.Lee, and D.M.Cyr (2003).
Mechanisms for regulation of Hsp70 function by Hsp40.

Cell Stress Chaperones, 8, 309-316.

12820650 K.Krzewski, D.Kunikowska, J.Wysocki, A.Kotlarz, P.Thompkins, W.Ashraf, N.Lindsey, S.Picksley, R.Głośnicka, and B.Lipińska (2003).
Characterization of the anti-DnaJ monoclonal antibodies and their use to compare immunological properties of DnaJ and its human homologue HDJ-1.

Cell Stress Chaperones, 8, 8.

12941935 K.Linke, T.Wolfram, J.Bussemer, and U.Jakob (2003).
The roles of the two zinc binding sites in DnaJ.

J Biol Chem, 278, 44457-44466.

12718534 S.J.Landry (2003).
Structure and energetics of an allele-specific genetic interaction between dnaJ and dnaK: correlation of nuclear magnetic resonance chemical shift perturbations in the J-domain of Hsp40/DnaJ with binding affinity for the ATPase domain of Hsp70/DnaK.

Biochemistry, 42, 4926-4936.

11921304 C.Lee, and Y.Cho (2002).
Interactions of SV40 large T antigen and other viral proteins with retinoblastoma tumour suppressor.

Rev Med Virol, 12, 81-92.

12040123 C.S.Sullivan, and J.M.Pipas (2002).
T antigens of simian virus 40: molecular chaperones for viral replication and tumorigenesis.

Microbiol Mol Biol Rev, 66, 179-202.

11929994 M.Gautschi, A.Mun, S.Ross, and S.Rospert (2002).
A functional chaperone triad on the yeast ribosome.

Proc Natl Acad Sci U S A, 99, 4209-4214.

12454054 P.Genevaux, F.Schwager, C.Georgopoulos, and W.L.Kelley (2002).
Scanning mutagenesis identifies amino acid residues essential for the in vivo activity of the Escherichia coli DnaJ (Hsp40) J-domain.

Genetics, 162, 1045-1053.

11919183 S.Lee, C.Y.Fan, J.M.Younger, H.Ren, and D.M.Cyr (2002).
Identification of essential residues in the type II Hsp40 Sis1 that function in polypeptide binding.

J Biol Chem, 277, 21675-21682.

11854498 S.W.Fewell, J.M.Pipas, and J.L.Brodsky (2002).
Mutagenesis of a functional chimeric gene in yeast identifies mutations in the simian virus 40 large T antigen J domain.

Proc Natl Acad Sci U S A, 99, 2002-2007.

11160729 H.Li, K.Söderbärg, H.Houshmand, Z.Y.You, and G.Magnusson (2001).
Effect on polyomavirus T-antigen function of mutations in a conserved leucine-rich segment of the DnaJ domain.

J Virol, 75, 2253-2261.

11226179 H.Y.Kim, B.Y.Ahn, and Y.Cho (2001).
Structural basis for the inactivation of retinoblastoma tumor suppressor by SV40 large T antigen.

EMBO J, 20, 295-304.

PDB code: 1gh6

11395418 J.Frydman (2001).
Folding of newly translated proteins in vivo: the role of molecular chaperones.

Annu Rev Biochem, 70, 603-647.

11584023 P.P.Lau, H.Villanueva, K.Kobayashi, M.Nakamuta, B.H.Chang, and L.Chan (2001).
A DnaJ protein, apobec-1-binding protein-2, modulates apolipoprotein B mRNA editing.

J Biol Chem, 276, 46445-46452.

11700281 S.W.Fewell, K.J.Travers, J.S.Weissman, and J.L.Brodsky (2001).
The action of molecular chaperones in the early secretory pathway.

Annu Rev Genet, 35, 149-191.

11048657 F.Hennessy, M.E.Cheetham, H.W.Dirr, and G.L.Blatch (2000).
Analysis of the levels of conservation of the J domain among the various types of DnaJ-like proteins.

Cell Stress Chaperones, 5, 347-358.

10777498 M.Chevalier, H.Rhee, E.C.Elguindi, and S.Y.Blond (2000).
Interaction of murine BiP/GRP78 with the DnaJ homologue MTJ1.

J Biol Chem, 275, 19620-19627.

10593983 A.A.Michels, B.Kanon, O.Bensaude, and H.H.Kampinga (1999).
Heat shock protein (Hsp) 40 mutants inhibit Hsp70 in mammalian cells.

J Biol Chem, 274, 36757-36763.

10082511 E.Sock, J.Enderich, and M.Wegner (1999).
The J domain of papovaviral large tumor antigen is required for synergistic interaction with the POU-domain protein Tst-1/Oct6/SCIP.

Mol Cell Biol, 19, 2455-2464.

10210198 K.Huang, J.M.Flanagan, and J.H.Prestegard (1999).
The influence of C-terminal extension on the structure of the "J-domain" in E. coli DnaJ.

Protein Sci, 8, 203-214.

PDB codes: 1bq0 1bqz

10447671 M.Münchbach, P.Dainese, W.Staudenmann, F.Narberhaus, and P.James (1999).
Proteome analysis of heat shock protein expression in Bradyrhizobium japonicum.

Eur J Biochem, 264, 39-48.

10523664 W.Yan, and E.A.Craig (1999).
The glycine-phenylalanine-rich region determines the specificity of the yeast Hsp40 Sis1.

Mol Cell Biol, 19, 7751-7758.

9852006 J.J.Silberg, K.G.Hoff, and L.E.Vickery (1998).
The Hsc66-Hsc20 chaperone system in Escherichia coli: chaperone activity and interactions with the DnaK-DnaJ-grpE system.

J Bacteriol, 180, 6617-6624.

9620985 J.L.Brodsky, and J.M.Pipas (1998).
Polyomavirus T antigens: molecular chaperones for multiprotein complexes.

J Virol, 72, 5329-5334.

9804845 J.S.Liu, S.R.Kuo, A.M.Makhov, D.M.Cyr, J.D.Griffith, T.R.Broker, and L.T.Chow (1998).
Human Hsp70 and Hsp40 chaperone proteins facilitate human papillomavirus-11 E1 protein binding to the origin and stimulate cell-free DNA replication.

J Biol Chem, 273, 30704-30712.

9791178 L.Goffin, and C.Georgopoulos (1998).
Genetic and biochemical characterization of mutations affecting the carboxy-terminal domain of the Escherichia coli molecular chaperone DnaJ.

Mol Microbiol, 30, 329-340.

9600925 M.K.Greene, K.Maskos, and S.J.Landry (1998).
Role of the J-domain in the cooperation of Hsp40 with Hsp70.

Proc Natl Acad Sci U S A, 95, 6108-6113.

9809521 T.Rich, U.Grüneberg, and J.Trowsdale (1998).
Heat shock proteins, HLA-DR and rheumatoid arthritis.

Nat Med, 4, 1210-1211.

9488737 Z.Lu, and D.M.Cyr (1998).
The conserved carboxyl terminus and zinc finger-like domain of the co-chaperone Ydj1 assist Hsp70 in protein folding.

J Biol Chem, 273, 5970-5978.

9234732 A.Srinivasan, A.J.McClellan, J.Vartikar, I.Marks, P.Cantalupo, Y.Li, P.Whyte, K.Rundell, J.L.Brodsky, and J.M.Pipas (1997).
The amino-terminal transforming region of simian virus 40 large T and small t antigens functions as a J domain.

Mol Cell Biol, 17, 4761-4773.

9235966 E.Ungewickell, H.Ungewickell, and S.E.Holstein (1997).
Functional interaction of the auxilin J domain with the nucleotide- and substrate-binding modules of Hsc70.

J Biol Chem, 272, 19594-19600.

9300502 J.R.Cupp-Vickery, and L.E.Vickery (1997).
Crystallization and preliminary X-ray crystallographic properties of Hsc20, a J-motif co-chaperone protein from Escherichia coli.

Protein Sci, 6, 2028-2030.

9144776 L.E.Vickery, J.J.Silberg, and D.T.Ta (1997).
Hsc66 and Hsc20, a new heat shock cognate molecular chaperone system from Escherichia coli.

Protein Sci, 6, 1047-1056.

9395474 L.H.Chamberlain, and R.D.Burgoyne (1997).
The molecular chaperone function of the secretory vesicle cysteine string proteins.

J Biol Chem, 272, 31420-31426.

9371601 Q.Sheng, D.Denis, M.Ratnofsky, T.M.Roberts, J.A.DeCaprio, and B.Schaffhausen (1997).
The DnaJ domain of polyomavirus large T antigen is required to regulate Rb family tumor suppressor function.

J Virol, 71, 9410-9416.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.