PDBsum entry 1ovx

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protein metals Protein-protein interface(s) links
Metal binding protein PDB id
Protein chains
38 a.a. *
_ZN ×2
* Residue conservation analysis
PDB id:
Name: Metal binding protein
Title: Nmr structure of the e. Coli clpx chaperone zinc binding dom
Structure: Atp-dependent clp protease atp-binding subunit cl chain: a, b. Fragment: n-terminal domain (residues 1-60). Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: clpx. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 1 models
Authors: L.W.Donaldson,J.Kwan,U.Wojtyra,W.A.Houry
Key ref:
L.W.Donaldson et al. (2003). Solution structure of the dimeric zinc binding domain of the chaperone ClpX. J Biol Chem, 278, 48991-48996. PubMed id: 14525985 DOI: 10.1074/jbc.M307826200
27-Mar-03     Release date:   30-Dec-03    
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Protein chains
Pfam   ArchSchema ?
P0A6H1  (CLPX_ECOLI) -  ATP-dependent Clp protease ATP-binding subunit ClpX
424 a.a.
38 a.a.
Key:    PfamA domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     protein dimerization activity     2 terms  


DOI no: 10.1074/jbc.M307826200 J Biol Chem 278:48991-48996 (2003)
PubMed id: 14525985  
Solution structure of the dimeric zinc binding domain of the chaperone ClpX.
L.W.Donaldson, U.Wojtyra, W.A.Houry.
ClpX (423 amino acids), a member of the Clp/Hsp100 family of molecular chaperones and the protease, ClpP, comprise a multimeric complex supporting targeted protein degradation in Escherichia coli. The ClpX sequence consists of an NH2-terminal zinc binding domain (ZBD) and a COOH-terminal ATPase domain. Earlier, we have demonstrated that the zinc binding domain forms a constitutive dimer that is essential for the degradation of some ClpX substrates such as gammaO and MuA but is not required for the degradation of other substrates such as green fluorescent protein-SsrA. In this report, we present the NMR solution structure of the zinc binding domain dimer. The monomer fold reveals that ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions. However, the dimeric ZBD structure is not related to any protein structure in the Protein Data Bank. A trimer-of-dimers model of ZBD is presented, which might reflect the closed state of the ClpX hexamer.
  Selected figure(s)  
Figure 2.
FIG. 2. Structure of ZBD. A, backbone superposition of 25 low energy structures of the ZBD homodimer. B, ribbon representation of the lowest energy structure. Helices are colored blue, and strands are colored red. Zn(II) atoms are shown as yellow spheres, and the cysteines involved in chelating the Zn(II) are drawn as yellow sticks. C, hydrophobic residues forming the core of the ZBD dimer are shown as space-filling models. These residues are Phe^16, Ile^28, Val33, Ile^35, Val40, and Ile^47. Residues from the left monomer are colored orange, while those from the right monomer are colored red.
Figure 5.
FIG. 5. Comparison of the NH[2]-terminal domains of ClpX, ClpA, and ClpB. Structures of the ZBD dimer, ClpA N-domain (Protein Data Bank code 1K6K [PDB] ) (30), and ClpB N-domain (Protein Data Bank code 1KHY [PDB] ) (51) are shown. Zn(II) atoms are drawn as spheres.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 48991-48996) copyright 2003.  
  Figures were selected by the author.  
    Author's comment    
  Comparison of the N-terminal domains of ClpX, ClpA, and ClpB. Structures of the ZBD dimer, ClpA N-domain (PDB: 1K6K), and ClpB N-domain (PDB: 1KHY) (51) are shown.
Note that Fig 5 is a corrected figure and not as it appears in the original paper.
Logan Donaldson / York University /

Literature references that cite this PDB file's key reference

  PubMed id Reference
21210168 I.Rose, G.Biuković, P.Aderhold, V.Müller, G.Grüber, and B.Averhoff (2011).
Identification and characterization of a unique, zinc-containing transport ATPase essential for natural transformation in Thermus thermophilus HB27.
  Extremophiles, 15, 191-202.  
20014030 T.Chowdhury, P.Chien, S.Ebrahim, R.T.Sauer, and T.A.Baker (2010).
Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species.
  Protein Sci, 19, 242-254.  
19914167 S.E.Glynn, A.Martin, A.R.Nager, T.A.Baker, and R.T.Sauer (2009).
Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine.
  Cell, 139, 744-756.
PDB codes: 3hte 3hws
18421150 E.Y.Park, and H.K.Song (2008).
A degradation signal recognition in prokaryotes.
  J Synchrotron Radiat, 15, 246-249.  
17090685 G.Thibault, J.Yudin, P.Wong, V.Tsitrin, R.Sprangers, R.Zhao, and W.A.Houry (2006).
Specificity in substrate and cofactor recognition by the N-terminal domain of the chaperone ClpX.
  Proc Natl Acad Sci U S A, 103, 17724-17729.  
16810315 G.Thibault, Y.Tsitrin, T.Davidson, A.Gribun, and W.A.Houry (2006).
Large nucleotide-dependent movement of the N-terminal domain of the ClpX chaperone.
  EMBO J, 25, 3367-3376.  
15601709 J.L.Camberg, and M.Sandkvist (2005).
Molecular analysis of the Vibrio cholerae type II secretion ATPase EpsE.
  J Bacteriol, 187, 249-256.  
14967151 D.N.Bolon, D.A.Wah, G.L.Hersch, T.A.Baker, and R.T.Sauer (2004).
Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: a protein-design study.
  Mol Cell, 13, 443-449.  
14962378 M.R.Maurizi, and D.Xia (2004).
Protein binding and disruption by Clp/Hsp100 chaperones.
  Structure, 12, 175-183.  
15501681 N.J.Marianayagam, M.Sunde, and J.M.Matthews (2004).
The power of two: protein dimerization in biology.
  Trends Biochem Sci, 29, 618-625.  
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