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PDBsum entry 2ds8

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protein ligands metals Protein-protein interface(s) links
Metal binding protein, protein binding PDB id
2ds8
Jmol
Contents
Protein chains
43 a.a. *
Ligands
ALA-LEU-ARG-VAL-
VAL-LYS
×2
Metals
_ZN ×2
Waters ×86
* Residue conservation analysis
PDB id:
2ds8
Name: Metal binding protein, protein binding
Title: Structure of the zbd-xb complex
Structure: Atp-dependent clp protease atp-binding subunit clpx. Chain: a, b. Fragment: zinc binding domain(zbd). Synonym: clpx. Engineered: yes. Sspb-tail peptide. Chain: p, q. Synonym: xb.
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: xb peptide (apalrvvk) is synthesized. Except the first alanine, the sequence occurs naturally in e. Coli sspb
Resolution:
1.60Å     R-factor:   0.201     R-free:   0.226
Authors: E.Y.Park,B.G.Lee,S.B.Hong,H.W.Kim,H.K.Song
Key ref:
E.Y.Park et al. (2007). Structural basis of SspB-tail recognition by the zinc binding domain of ClpX. J Mol Biol, 367, 514-526. PubMed id: 17258768 DOI: 10.1016/j.jmb.2007.01.003
Date:
22-Jun-06     Release date:   13-Feb-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A6H1  (CLPX_ECOLI) -  ATP-dependent Clp protease ATP-binding subunit ClpX
Seq:
Struc:
424 a.a.
43 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
DOI no: 10.1016/j.jmb.2007.01.003 J Mol Biol 367:514-526 (2007)
PubMed id: 17258768  
 
 
Structural basis of SspB-tail recognition by the zinc binding domain of ClpX.
E.Y.Park, B.G.Lee, S.B.Hong, H.W.Kim, H.Jeon, H.K.Song.
 
  ABSTRACT  
 
The degradation of ssrA(AANDENYALAA)-tagged proteins in the bacterial cytosol is carried out by the ClpXP protease and is markedly stimulated by the SspB adaptor protein. It has previously been reported that the amino-terminal zinc-binding domain of ClpX (ZBD) is involved in complex formation with the SspB-tail (XB: ClpX-binding motif). In an effort to better understand the recognition of SspB by ClpX and the mechanism of delivery of ssrA-tagged substrates to ClpXP, we have determined the structures of ZBD alone at 1.5, 2.0, and 2.5 A resolution in each different crystal form and also in complex with XB peptide at 1.6 A resolution. The XB peptide forms an antiparallel beta-sheet with two beta-strands of ZBD, and the structure shows a 1:1 stoichiometric complex between ZBD and XB, suggesting that there are two independent SspB-tail-binding sites in ZBD. The high-resolution ZBD:XB complex structure, in combination with biochemical analyses, can account for key determinants in the recognition of the SspB-tail by ClpX and sheds light on the mechanism of delivery of target proteins to the prokaryotic degradation machine.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structure of the ZBD-XB complex. (a) Ribbon diagram showing the dimeric ZBD-XB complex structure viewed along the non-crystallographic 2-fold molecular symmetry axis. Each monomer in the ZBD is colored green and yellow. The bound XB peptide and zinc ion are colored salmon and purple, respectively. The N and C termini of the ZBD are labeled, as are the first and last residues of the XB peptide (160p and 165p). (b) Ribbon diagram showing the monomer of the ZBD and details of bound XB peptide. The view is almost the same as in (a). Side-chains of five cysteine in the ZBD and XB peptide are shown, and secondary structural elements of the ZBD and the residues drawn are labeled. (c) Plot of the difference between free and complexed ZBD models. The RMS differences for the main chain atoms of each residue are plotted as a function of residue number (free ZBD versus XB-ZBD complex, blue line; free ZBD versus ZBD NMR structure, red line). The secondary structural elements are indicated. (d) Backbone superposition of free (green), free NMR (yellow), and the XB complex (salmon) structure. N and C termini of the ZBD and the regions showing significant structural movement are marked with transparent ovals. Figure 2. Structure of the ZBD-XB complex. (a) Ribbon diagram showing the dimeric ZBD-XB complex structure viewed along the non-crystallographic 2-fold molecular symmetry axis. Each monomer in the ZBD is colored green and yellow. The bound XB peptide and zinc ion are colored salmon and purple, respectively. The N and C termini of the ZBD are labeled, as are the first and last residues of the XB peptide (160p and 165p). (b) Ribbon diagram showing the monomer of the ZBD and details of bound XB peptide. The view is almost the same as in (a). Side-chains of five cysteine in the ZBD and XB peptide are shown, and secondary structural elements of the ZBD and the residues drawn are labeled. (c) Plot of the difference between free and complexed ZBD models. The RMS differences for the main chain atoms of each residue are plotted as a function of residue number (free ZBD versus XB-ZBD complex, blue line; free ZBD versus ZBD NMR structure, red line). The secondary structural elements are indicated. (d) Backbone superposition of free (green), free NMR (yellow), and the XB complex (salmon) structure. N and C termini of the ZBD and the regions showing significant structural movement are marked with transparent ovals.
Figure 3.
Figure 3. XB peptide-binding site of the ZBD. (a) Schematic diagram showing interactions between the ZBD and XB peptide. Hydrophobic interactions are denoted by red starbursts and broken lines; hydrogen-bonding interactions by black broken lines. This panel was drawn using LIGPLOT.^52 (b) A view of the electron density map showing the bound XB peptide and its binding site in the ZBD. The |F[o]–F[c]| map (dark grey color) was calculated prior to inclusion of the illustrated XB peptide residues in the model. This map was calculated using 30–1.6 Å data and is contoured at 2.7 σ. This panel was drawn using PyMOL [http://pymol.sourceforge.net/]. Figure 3. XB peptide-binding site of the ZBD. (a) Schematic diagram showing interactions between the ZBD and XB peptide. Hydrophobic interactions are denoted by red starbursts and broken lines; hydrogen-bonding interactions by black broken lines. This panel was drawn using LIGPLOT.[3]^52 (b) A view of the electron density map showing the bound XB peptide and its binding site in the ZBD. The |F[o]–F[c]| map (dark grey color) was calculated prior to inclusion of the illustrated XB peptide residues in the model. This map was calculated using 30–1.6 Å data and is contoured at 2.7 σ. This panel was drawn using PyMOL [http://pymol.sourceforge.net/].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 367, 514-526) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20305655 B.G.Lee, E.Y.Park, K.E.Lee, H.Jeon, K.H.Sung, H.Paulsen, H.Rübsamen-Schaeff, H.Brötz-Oesterhelt, and H.K.Song (2010).
Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism.
  Nat Struct Mol Biol, 17, 471-478.
PDB codes: 3ktg 3kth 3kti 3ktj 3ktk
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.  
19549779 J.H.Davis, T.A.Baker, and R.T.Sauer (2009).
Engineering synthetic adaptors and substrates for controlled ClpXP degradation.
  J Biol Chem, 284, 21848-21855.  
19609260 J.Kirstein, N.Molière, D.A.Dougan, and K.Turgay (2009).
Adapting the machine: adaptor proteins for Hsp100/Clp and AAA+ proteases.
  Nat Rev Microbiol, 7, 589-599.  
19388025 O.Sénèque, E.Bonnet, F.L.Joumas, and J.M.Latour (2009).
Cooperative metal binding and helical folding in model peptides of treble-clef zinc fingers.
  Chemistry, 15, 4798-4810.  
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
19074380 S.K.Garg, S.Kommineni, L.Henslee, Y.Zhang, and P.Zuber (2009).
The YjbH protein of Bacillus subtilis enhances ClpXP-catalyzed proteolysis of Spx.
  J Bacteriol, 191, 1268-1277.  
19912542 Z.Ge, and A.W.Karzai (2009).
Co-evolution of multipartite interactions between an extended tmRNA tag and a robust Lon protease in Mycoplasma.
  Mol Microbiol, 74, 1083-1099.  
18406325 A.H.Abdelhakim, E.C.Oakes, R.T.Sauer, and T.A.Baker (2008).
Unique contacts direct high-priority recognition of the tetrameric Mu transposase-DNA complex by the AAA+ unfoldase ClpX.
  Mol Cell, 30, 39-50.  
18421150 E.Y.Park, and H.K.Song (2008).
A degradation signal recognition in prokaryotes.
  J Synchrotron Radiat, 15, 246-249.  
  18811726 K.L.Griffith, and A.D.Grossman (2008).
Inducible protein degradation in Bacillus subtilis using heterologous peptide tags and adaptor proteins to target substrates to the protease ClpXP.
  Mol Microbiol, 70, 1012-1025.  
18689473 L.A.Simmons, A.D.Grossman, and G.C.Walker (2008).
Clp and Lon proteases occupy distinct subcellular positions in Bacillus subtilis.
  J Bacteriol, 190, 6758-6768.  
17317664 K.E.McGinness, D.N.Bolon, M.Kaganovich, T.A.Baker, and R.T.Sauer (2007).
Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery.
  J Biol Chem, 282, 11465-11473.  
17600141 L.Cheng, T.A.Naumann, A.R.Horswill, S.J.Hong, B.J.Venters, J.W.Tomsho, S.J.Benkovic, and K.C.Keiler (2007).
Discovery of antibacterial cyclic peptides that inhibit the ClpXP protease.
  Protein Sci, 16, 1535-1542.  
17827297 Y.Zhang, and P.Zuber (2007).
Requirement of the zinc-binding domain of ClpX for Spx proteolysis in Bacillus subtilis and effects of disulfide stress on ClpXP activity.
  J Bacteriol, 189, 7669-7680.  
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.