PDBsum entry 1jbk

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protein metals links
Chaperone PDB id
Protein chain
189 a.a. *
Waters ×296
* Residue conservation analysis
PDB id:
Name: Chaperone
Title: Crystal structure of the first nucelotide binding domain of clpb
Structure: Clpb protein. Chain: a. Fragment: first nucleotide binding domain (residues 159- 351). Synonym: heat shock protein f84.1. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.80Å     R-factor:   0.222     R-free:   0.247
Authors: L.Jingzhi,S.Bingdong
Key ref:
J.Li and B.Sha (2002). Crystal structure of E. coli Hsp100 ClpB nucleotide-binding domain 1 (NBD1) and mechanistic studies on ClpB ATPase activity. J Mol Biol, 318, 1127-1137. PubMed id: 12054807 DOI: 10.1016/S0022-2836(02)00188-2
05-Jun-01     Release date:   05-Jun-02    
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Protein chain
Pfam   ArchSchema ?
P63284  (CLPB_ECOLI) -  Chaperone protein ClpB
857 a.a.
189 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     3 terms  


DOI no: 10.1016/S0022-2836(02)00188-2 J Mol Biol 318:1127-1137 (2002)
PubMed id: 12054807  
Crystal structure of E. coli Hsp100 ClpB nucleotide-binding domain 1 (NBD1) and mechanistic studies on ClpB ATPase activity.
J.Li, B.Sha.
E. coli Hsp100 ClpB was recently identified as a critical part in a multi-chaperone system to play important roles in protein folding, protein transport and degradation in cell physiology. ClpB contains two nucleotide-binding domains (NBD1 and NBD2) within their primary sequences. NBD1 and NBD2 of ClpB can be classified as members of the large ATPase family known as ATPases associated with various cellular activities (AAA). To investigate how ClpB performs its ATPase activities for its chaperone activity, we have determined the crystal structure of ClpB nucleotide-binding domain 1 (NBD1) by MAD method to 1.80 A resolution. The NBD1 monomer structure contains one domain that comprises 11 alpha-helices and six beta-strands. When compared with the typical AAA structures, the crystal structure of ClpB NBD1 reveals a novel AAA topology with six-stranded beta-sheet as its core. The N-terminal portion of NBD1 structure has an extra beta-strand flanked by two extra alpha-helices that are not present in other AAA structures. Moreover, the NBD1 structure does not have a C-terminal helical domain as other AAA proteins do. No nucleotide molecule is bound with ClpB NBD1 in the crystal structure probably due to lack of the C-terminal helix domain in the structure. Isothermal titration calorimetry (ITC) studies of ClpB NBD1 and other ClpB deletion mutations showed that either ClpB NBD1 or NBD2 alone does not bind to nucleotides. However, ClpB NBD2 combined with ClpB C-terminal fragment can interact with one ADP or ATP molecule. ITC data also indicated that full-length ClpB could bind two ADP molecules or one ATP analogue ATPgammaS molecule. Further ATPase activity studies of ClpB and ClpB deletion mutants showed that only wild-type ClpB have ATPase activity. None of ClpB NBD1 domain, NBD2 domain and NBD2 with C-terminal fragment has detectable ATPase activities. On the basis of our structural and mutagenesis data, we proposed a "see-saw" model to illustrate the mechanisms by which ClpB performs its ATPase activities for chaperone functions.
  Selected figure(s)  
Figure 2.
Figure 2. Sequence alignment for NBD1 among Class I Hsp100 proteins. The NBD1 sequence of E. coli ClpB is aligned by program Pileup with that of Mycobacterium leprae Hsp100 P24428, S. cerevisae Hsp104, E. coli Hsp100 ClpA and A. thaliana ERD1 D17582. The residue numbers of ClpB are labeled on top of the sequences. The conserved Walker A and B motifs are shown in bold.
Figure 4.
Figure 4. Schematic drawings of full-length ClpB and its deletion mutants. The ClpB N-terminal fragment is denoted by a shaded box. The ClpB NBD1 domain and NBD2 domain are represented by pink and blue boxes. The ClpB C-terminal fragment is shown by a green box. The linker region between NBD1 and NBD2 domains is indicated by a continuous line. The residue numbers of the various domains are drawn on top of the full-length ClpB.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 1127-1137) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19714768 S.Zietkiewicz, M.J.Slusarz, R.Slusarz, K.Liberek, and S.Rodziewicz-Motowidło (2010).
Conformational stability of the full-atom hexameric model of the ClpB chaperone from Escherichia coli.
  Biopolymers, 93, 47-60.  
19177562 M.Nagy, H.C.Wu, Z.Liu, S.Kedzierska-Mieszkowska, and M.Zolkiewski (2009).
Walker-A threonine couples nucleotide occupancy with the chaperone activity of the AAA+ ATPase ClpB.
  Protein Sci, 18, 287-293.  
19465386 S.J.Suhrer, M.Wiederstein, M.Gruber, and M.J.Sippl (2009).
COPS--a novel workbench for explorations in fold space.
  Nucleic Acids Res, 37, W539-W544.  
  17768355 S.Lee, and F.T.Tsai (2007).
Crystallization and preliminary X-ray crystallographic analysis of a 40 kDa N-terminal fragment of the yeast prion-remodeling factor Hsp104.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 784-786.  
16307477 C.Schlieker, H.Zentgraf, P.Dersch, and A.Mogk (2005).
ClpV, a unique Hsp100/Clp member of pathogenic proteobacteria.
  Biol Chem, 386, 1115-1127.  
15208691 C.Schlieker, J.Weibezahn, H.Patzelt, P.Tessarz, C.Strub, K.Zeth, A.Erbse, J.Schneider-Mergener, J.W.Chin, P.G.Schultz, B.Bukau, and A.Mogk (2004).
Substrate recognition by the AAA+ chaperone ClpB.
  Nat Struct Mol Biol, 11, 607-615.  
14728719 J.Weibezahn, B.Bukau, and A.Mogk (2004).
Unscrambling an egg: protein disaggregation by AAA+ proteins.
  Microb Cell Fact, 3, 1.  
12624113 A.Mogk, C.Schlieker, C.Strub, W.Rist, J.Weibezahn, and B.Bukau (2003).
Roles of individual domains and conserved motifs of the AAA+ chaperone ClpB in oligomerization, ATP hydrolysis, and chaperone activity.
  J Biol Chem, 278, 17615-17624.  
12623019 J.Li, and B.Sha (2003).
Crystal structure of the E. coli Hsp100 ClpB N-terminal domain.
  Structure, 11, 323-328.  
14732929 M.J.Cliff, and J.E.Ladbury (2003).
A survey of the year 2002 literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 16, 383-391.  
12717012 R.E.Burton, T.A.Baker, and R.T.Sauer (2003).
Energy-dependent degradation: Linkage between ClpX-catalyzed nucleotide hydrolysis and protein-substrate processing.
  Protein Sci, 12, 893-902.  
14640692 S.Kedzierska, V.Akoev, M.E.Barnett, and M.Zolkiewski (2003).
Structure and function of the middle domain of ClpB from Escherichia coli.
  Biochemistry, 42, 14242-14248.  
14567920 S.Lee, M.E.Sowa, Y.H.Watanabe, P.B.Sigler, W.Chiu, M.Yoshida, and F.T.Tsai (2003).
The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state.
  Cell, 115, 229-240.
PDB code: 1qvr
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.