Structural basis of SspB-tail recognition by the zinc binding domain of ClpX

J Mol Biol. 2007 Mar 23;367(2):514-26. doi: 10.1016/j.jmb.2007.01.003. Epub 2007 Jan 9.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • ATPases Associated with Diverse Cellular Activities
  • Adenosine Triphosphatases / chemistry*
  • Adenosine Triphosphatases / genetics
  • Binding Sites
  • Carrier Proteins / chemistry*
  • Carrier Proteins / genetics
  • Endopeptidase Clp / chemistry*
  • Endopeptidase Clp / genetics
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Models, Molecular*
  • Molecular Chaperones / chemistry*
  • Molecular Chaperones / genetics
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / genetics
  • Substrate Specificity
  • Zinc / chemistry*

Substances

  • Carrier Proteins
  • Escherichia coli Proteins
  • Molecular Chaperones
  • Recombinant Fusion Proteins
  • sspB protein, E coli
  • Endopeptidase Clp
  • Adenosine Triphosphatases
  • ClpX protein, E coli
  • ATPases Associated with Diverse Cellular Activities
  • Zinc

Associated data

  • PDB/2DS5
  • PDB/2DS6
  • PDB/2DS7
  • PDB/2DS8