3HDI image
Deposition Date 2009-05-07
Release Date 2009-12-08
Last Version Date 2023-09-06
Entry Detail
PDB ID:
3HDI
Keywords:
Title:
Crystal structure of Bacillus halodurans metallo peptidase
Biological Source:
Source Organism:
Bacillus halodurans C-125 (Taxon ID: 272558)
(Taxon ID: )
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.70 Å
R-Value Free:
0.26
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Processing protease
Gene (Uniprot):BH2405
Chain IDs:A, B
Chain Length:421
Number of Molecules:2
Biological Source:Bacillus halodurans C-125
Polymer Type:polypeptide(L)
Molecule:Synthetic peptide
Chain IDs:C, D
Chain Length:17
Number of Molecules:2
Biological Source:
Primary Citation
Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case.
Structure 17 1465 1475 (2009)
PMID: 19913481 DOI: 10.1016/j.str.2009.09.009

Abstact

The M16 family of zinc peptidases comprises a pair of homologous domains that form two halves of a "clam-shell" surrounding the active site. The M16A and M16C subfamilies form one class ("peptidasomes"): they degrade 30-70 residue peptides, and adopt both open and closed conformations. The eukaryotic M16B subfamily forms a second class ("processing proteases"): they adopt a single partly-open conformation that enables them to cleave signal sequences from larger proteins. Here, we report the solution and crystal structures of a prokaryotic M16B peptidase, and demonstrate that it has features of both classes: thus, it forms stable "open" homodimers in solution that resemble the processing proteases; but the clam-shell closes upon binding substrate, a feature of the M16A/C peptidasomes. Moreover, clam-shell closure is required for proteolytic activity. We predict that other prokaryotic M16B family members will form dimeric peptidasomes, and propose a model for the evolution of the M16 family.

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