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PDBsum entry 1bpr
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Molecular chaperone
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PDB id
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1bpr
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Contents |
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* Residue conservation analysis
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DOI no:
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Biochemistry
37:7929-7940
(1998)
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PubMed id:
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NMR solution structure of the 21 kDa chaperone protein DnaK substrate binding domain: a preview of chaperone-protein interaction.
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H.Wang,
A.V.Kurochkin,
Y.Pang,
W.Hu,
G.C.Flynn,
E.R.Zuiderweg.
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ABSTRACT
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The solution structure of the 21 kDa substrate-binding domain of the Escherichia
coli Hsp70-chaperone protein DnaK (DnaK 386-561) has been determined to a
precision of 1.00 A (backbone of the beta-domain) from 1075 experimental
restraints obtained from multinuclear, multidimensional NMR experiments. The
domain is observed to bind to its own C-terminus and offers a preview of the
interaction of this chaperone with other proteins. The bound protein region is
tightly held at a single amino acid position (a leucyl residue) that is buried
in a deep pocket lined with conserved hydrophobic residues. A second hydrophobic
binding site was identified using paramagnetically labeled peptides. It is
located in a region close to the N-terminus of the domain and may constitute the
allosteric region that links substrate-binding affinity with nucleotide binding
in the Hsp70 chaperones.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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R.Schlecht,
A.H.Erbse,
B.Bukau,
and
M.P.Mayer
(2011).
Mechanics of Hsp70 chaperones enables differential interaction with client proteins.
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Nat Struct Mol Biol,
18,
345-351.
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M.Liebscher,
K.Haupt,
C.Yu,
G.Jahreis,
C.Lücke,
and
C.Schiene-Fischer
(2010).
Rational design of novel peptidic DnaK ligands.
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Chembiochem,
11,
1727-1737.
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M.Shida,
A.Arakawa,
R.Ishii,
S.Kishishita,
T.Takagi,
M.Kukimoto-Niino,
S.Sugano,
A.Tanaka,
M.Shirouzu,
and
S.Yokoyama
(2010).
Direct inter-subdomain interactions switch between the closed and open forms of the Hsp70 nucleotide-binding domain in the nucleotide-free state.
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Acta Crystallogr D Biol Crystallogr,
66,
223-232.
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PDB codes:
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A.Bhattacharya,
A.V.Kurochkin,
G.N.Yip,
Y.Zhang,
E.B.Bertelsen,
and
E.R.Zuiderweg
(2009).
Allostery in Hsp70 chaperones is transduced by subdomain rotations.
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J Mol Biol,
388,
475-490.
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E.B.Bertelsen,
L.Chang,
J.E.Gestwicki,
and
E.R.Zuiderweg
(2009).
Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate.
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Proc Natl Acad Sci U S A,
106,
8471-8476.
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PDB code:
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J.P.Schuermann,
J.Jiang,
J.Cuellar,
O.Llorca,
L.Wang,
L.E.Gimenez,
S.Jin,
A.B.Taylor,
B.Demeler,
K.A.Morano,
P.J.Hart,
J.M.Valpuesta,
E.M.Lafer,
and
R.Sousa
(2008).
Structure of the Hsp110:Hsc70 nucleotide exchange machine.
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Mol Cell,
31,
232-243.
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PDB code:
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F.Moro,
V.Fernández-Sáiz,
and
A.Muga
(2006).
The allosteric transition in DnaK probed by infrared difference spectroscopy. Concerted ATP-induced rearrangement of the substrate binding domain.
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Protein Sci,
15,
223-233.
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J.F.Swain,
E.G.Schulz,
and
L.M.Gierasch
(2006).
Direct comparison of a stable isolated Hsp70 substrate-binding domain in the empty and substrate-bound states.
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J Biol Chem,
281,
1605-1611.
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J.Jiang,
E.M.Lafer,
and
R.Sousa
(2006).
Crystallization of a functionally intact Hsc70 chaperone.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
62,
39-43.
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L.Worrall,
and
M.D.Walkinshaw
(2006).
Crystallization and X-ray data analysis of the 10 kDa C-terminal lid subdomain from Caenorhabditis elegans Hsp70.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
62,
938-943.
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V.Fernández-Sáiz,
F.Moro,
J.M.Arizmendi,
S.P.Acebrón,
and
A.Muga
(2006).
Ionic contacts at DnaK substrate binding domain involved in the allosteric regulation of lid dynamics.
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J Biol Chem,
281,
7479-7488.
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W.Rist,
C.Graf,
B.Bukau,
and
M.P.Mayer
(2006).
Amide hydrogen exchange reveals conformational changes in hsp70 chaperones important for allosteric regulation.
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J Biol Chem,
281,
16493-16501.
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F.Moro,
V.Fernández-Sáiz,
O.Slutsky,
A.Azem,
and
A.Muga
(2005).
Conformational properties of bacterial DnaK and yeast mitochondrial Hsp70. Role of the divergent C-terminal alpha-helical subdomain.
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FEBS J,
272,
3184-3196.
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J.Jiang,
K.Prasad,
E.M.Lafer,
and
R.Sousa
(2005).
Structural basis of interdomain communication in the Hsc70 chaperone.
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Mol Cell,
20,
513-524.
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PDB code:
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M.Kellett,
and
S.W.McKechnie
(2005).
A cluster of diagnostic Hsp68 amino acid sites that are identified in Drosophila from the melanogaster species group are concentrated around beta-sheet residues involved with substrate binding.
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Genome,
48,
226-233.
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M.P.Mayer,
and
B.Bukau
(2005).
Hsp70 chaperones: cellular functions and molecular mechanism.
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Cell Mol Life Sci,
62,
670-684.
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P.C.Aoto,
D.T.Ta,
J.R.Cupp-Vickery,
and
L.E.Vickery
(2005).
X-ray diffraction analysis of a crystal of HscA from Escherichia coli.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
715-717.
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F.Moro,
V.Fernández-Sáiz,
and
A.Muga
(2004).
The lid subdomain of DnaK is required for the stabilization of the substrate-binding site.
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J Biol Chem,
279,
19600-19606.
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J.J.Silberg,
T.L.Tapley,
K.G.Hoff,
and
L.E.Vickery
(2004).
Regulation of the HscA ATPase reaction cycle by the co-chaperone HscB and the iron-sulfur cluster assembly protein IscU.
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J Biol Chem,
279,
53924-53931.
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M.Revington,
T.M.Holder,
and
E.R.Zuiderweg
(2004).
NMR study of nucleotide-induced changes in the nucleotide binding domain of Thermus thermophilus Hsp70 chaperone DnaK: implications for the allosteric mechanism.
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J Biol Chem,
279,
33958-33967.
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T.L.Tapley,
and
L.E.Vickery
(2004).
Preferential substrate binding orientation by the molecular chaperone HscA.
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J Biol Chem,
279,
28435-28442.
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C.C.Chou,
F.Forouhar,
Y.H.Yeh,
H.L.Shr,
C.Wang,
and
C.D.Hsiao
(2003).
Crystal structure of the C-terminal 10-kDa subdomain of Hsc70.
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J Biol Chem,
278,
30311-30316.
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PDB code:
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K.G.Hoff,
J.R.Cupp-Vickery,
and
L.E.Vickery
(2003).
Contributions of the LPPVK motif of the iron-sulfur template protein IscU to interactions with the Hsc66-Hsc20 chaperone system.
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J Biol Chem,
278,
37582-37589.
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S.Y.Stevens,
S.Cai,
M.Pellecchia,
and
E.R.Zuiderweg
(2003).
The solution structure of the bacterial HSP70 chaperone protein domain DnaK(393-507) in complex with the peptide NRLLLTG.
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Protein Sci,
12,
2588-2596.
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PDB code:
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J.L.Urbauer,
M.F.Simeonov,
R.J.Urbauer,
K.Adelman,
J.M.Gilmore,
and
E.N.Brody
(2002).
Solution structure and stability of the anti-sigma factor AsiA: implications for novel functions.
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Proc Natl Acad Sci U S A,
99,
1831-1835.
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PDB code:
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M.G.Sehorn,
S.V.Slepenkov,
and
S.N.Witt
(2002).
Characterization of two partially unfolded intermediates of the molecular chaperone DnaK at low pH.
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Biochemistry,
41,
8499-8507.
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N.Tanaka,
S.Nakao,
H.Wadai,
S.Ikeda,
J.Chatellier,
and
S.Kunugi
(2002).
The substrate binding domain of DnaK facilitates slow protein refolding.
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Proc Natl Acad Sci U S A,
99,
15398-15403.
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A.P.Demchenko
(2001).
Recognition between flexible protein molecules: induced and assisted folding.
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J Mol Recognit,
14,
42-61.
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C.C.Chou,
C.Wang,
Y.J.Sun,
H.L.Shr,
and
C.D.Hsiao
(2001).
Crystallization and preliminary X-ray diffraction analysis of the 10 kDa C-terminal subdomain of 70 kDa heat-shock cognate protein.
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Acta Crystallogr D Biol Crystallogr,
57,
1928-1930.
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C.Pfund,
P.Huang,
N.Lopez-Hoyo,
and
E.A.Craig
(2001).
Divergent functional properties of the ribosome-associated molecular chaperone Ssb compared with other Hsp70s.
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Mol Biol Cell,
12,
3773-3782.
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J.D.Fox,
R.B.Kapust,
and
D.S.Waugh
(2001).
Single amino acid substitutions on the surface of Escherichia coli maltose-binding protein can have a profound impact on the solubility of fusion proteins.
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Protein Sci,
10,
622-630.
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J.Vijayalakshmi,
M.K.Mukhergee,
J.Graumann,
U.Jakob,
and
M.A.Saper
(2001).
The 2.2 A crystal structure of Hsp33: a heat shock protein with redox-regulated chaperone activity.
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Structure,
9,
367-375.
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PDB code:
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L.H.Hung,
G.Chaconas,
and
G.S.Shaw
(2000).
The solution structure of the C-terminal domain of the Mu B transposition protein.
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EMBO J,
19,
5625-5634.
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PDB code:
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L.Otvos,
I.O,
M.E.Rogers,
P.J.Consolvo,
B.A.Condie,
S.Lovas,
P.Bulet,
and
M.Blaszczyk-Thurin
(2000).
Interaction between heat shock proteins and antimicrobial peptides.
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Biochemistry,
39,
14150-14159.
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M.Chevalier,
H.Rhee,
E.C.Elguindi,
and
S.Y.Blond
(2000).
Interaction of murine BiP/GRP78 with the DnaJ homologue MTJ1.
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J Biol Chem,
275,
19620-19627.
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M.E.Gottesman,
and
W.A.Hendrickson
(2000).
Protein folding and unfolding by Escherichia coli chaperones and chaperonins.
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Curr Opin Microbiol,
3,
197-202.
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M.P.Mayer,
S.Rüdiger,
and
B.Bukau
(2000).
Molecular basis for interactions of the DnaK chaperone with substrates.
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Biol Chem,
381,
877-885.
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S.C.Jenkins,
R.E.March,
R.D.Campbell,
and
C.M.Milner
(2000).
A novel variant of the MHC-linked hsp70, hsp70-hom, is associated with rheumatoid arthritis.
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Tissue Antigens,
56,
38-44.
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S.Kimmins,
and
T.H.MacRae
(2000).
Maturation of steroid receptors: an example of functional cooperation among molecular chaperones and their associated proteins.
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Cell Stress Chaperones,
5,
76-86.
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E.B.Bertelsen,
H.Zhou,
D.F.Lowry,
G.C.Flynn,
and
F.W.Dahlquist
(1999).
Topology and dynamics of the 10 kDa C-terminal domain of DnaK in solution.
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Protein Sci,
8,
343-354.
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A.Artigues,
D.L.Crawford,
A.Iriarte,
and
M.Martinez-Carrion
(1998).
Divergent Hsc70 binding properties of mitochondrial and cytosolic aspartate aminotransferase. Implications for their segregation to different cellular compartments.
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J Biol Chem,
273,
33130-33134.
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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
codes are
shown on the right.
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Links
