PDBsum entry 2zl2

Hydrolase

PDB id: 2zl2

Contents

Protein chains

(+ 8 more) 174 a.a. *

Ligands

ASN-VAL-LEU-GLY ×6

GLY-PHE-THR-GLN

UNK-UNK-UNK

UNK-UNK-UNK-UNK

VAL-LEU-GLY-PHE

* Residue conservation analysis

PDB id:

2zl2

Name:

Hydrolase

Title:

Crystal structure of h.Pylori clpp in complex with the peptide nvlgftq

Structure:

Atp-dependent clp protease proteolytic subunit. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n. Synonym: endopeptidase clp. Engineered: yes. A peptide substrate-nvlgftq. Chain: o, p, q, t, u, v, w, x. Engineered: yes. A peptide substrate-nvlgftq for chain r and s. Chain: r, s.

Source:

Helicobacter pylori. Organism_taxid: 210. Gene: clpp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the peptide was chemically synthesized.. Other_details: the peptide was chemically synthesized.

Resolution:

2.50Å R-factor: 0.230 R-free: 0.274

Authors:

D.Y.Kim,K.K.Kim

Key ref:

D.Y.Kim and K.K.Kim (2008). The structural basis for the activation and peptide recognition of bacterial ClpP. J Mol Biol, 379, 760-771. PubMed id: 18468623 DOI: 10.1016/j.jmb.2008.04.036

Date:

02-Apr-08 Release date: 22-Apr-08

Protein chains

P56156  (CLPP_HELPY) -  ATP-dependent Clp protease proteolytic subunit from Helicobacter pylori (strain ATCC 700392 / 26695)

Seq: 196 a.a.

Struc: 174 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.92 - endopeptidase Clp.
• Reaction: Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are cleaved (such as succinyl-Leu-Tyr-|-NHMEC; and Leu-Tyr-Leu-|-Tyr-Trp, in which the cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp- bond also occurs).

DOI no: 10.1016/j.jmb.2008.04.036

J Mol Biol 379:760-771 (2008)

PubMed id: 18468623

The structural basis for the activation and peptide recognition of bacterial ClpP.

D.Y.Kim, K.K.Kim.

ABSTRACT

ClpP and its ATPase compartment, ClpX or ClpA, remove misfolded proteins in cells and are of utmost importance in protein quality control. The ring hexamers of ClpA or ClpX recognize, unfold, and translocate target substrates into the degradation chamber of the double-ring tetradecamer of ClpP. The overall reaction scheme catalyzed by ClpXP or ClpAP has been proposed; however, the molecular mechanisms associated with substrate recognition and degradation have not yet been clarified in detail. To investigate these mechanisms, we determined the crystal structures of ClpP from Helicobacter pylori in complex with product peptides bound to the active site as well as in the apo state. In the complex structure, the peptides are zipped with two antiparallel strands of ClpP and point to the adjacent active site, thus providing structural explanations for the broad substrate specificity, the product inhibition and the processive degradation of substrates in the chamber. The structures also suggest that substrate binding causes local conformational changes around the active site that ultimately induce the active conformation of ClpP.

Selected figure(s)

Figure 4.
Fig. 4. Rearrangement of residues in the active site of HpClpP by substrate binding. The apo-HpClpP and HpClpP/peptide complex (a) and apo-HpClpP S99A and HpClpP S99A/peptide complex (b) are overlapped by superposition of C^α traces. The apo form is green and the complex form is pink. The residues in the catalytic triad and peptides are represented by stick models. Possible bonds between Ser99OG (or Ala99CB) and His124NE2, and those between His124NE1 and Asp173OD are indicated by dashed lines and their distances are indicated in angstroms. (c) The C^α traces of six ClpPs near the catalytic triad are overlapped. Three residues in the catalytic triad are drawn as stick models. HpClpP and HpClpP/peptide complex are green and purple, respectively. ClpPs from E. coli, S. pneumoniae, P. falciparum and M. tuberculosis are brown (PDB accession number 1TYF), blue (1Y7O), orange (2F6I) and yellow (2CBY), respectively. (d) Structural overlap of HpClpP/peptide complex (pink) and EcClpP/inhibitor complex (cyan) near the active site. The residues of the catalytic triad and bound peptide and inhibitor are labeled and represented by stick models; those involved in substrate binding are also labeled and represented by stick models. The possible hydrogen bonds between HpClpP and peptide or EcClpP and inhibitor are depicted with dashed lines and their distances are indicated with the angstrom scale.

Figure 5.
Fig. 5. Peptide binding in the ClpP chamber and the model of progressive digestion of the substrate by ClpP. (a) The surface model of the proteolytic chamber of HpClpP with three peptides (tetra-Ala) bound to active sites. The surface of each subunit in HpClpP is represented by a different color and the red area represents the active-site Ser99. Tetrapeptides bound to the substrate-binding site are represented by gray stick models. (b) A linear polypeptide, a substrate translocated from ClpX to the ClpP chamber, is modeled and aligned along the active sites in the same color schemes and orientations as in (a). Each tetrapeptide shown in (a) is extended by adding three more amino acids. The resulting heptapeptides are connected to form a long linear peptide. The possible cleavage sites are indicated by cyan arrows. In this binding mode, a heptapeptide could be the cleavage product since it is almost the same size as the gap between adjacent active sites in the extended conformation.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 379, 760-771) copyright 2008.

Figures were selected by an automated process.