3HDI

Crystal structure of Bacillus halodurans metallo peptidase

Summary for 3HDI

• Entry DOI: 10.2210/pdb3hdi/pdb
• Descriptor: Processing protease, Synthetic peptide, COBALT (II) ION, ... (5 entities in total)
• Functional Keywords: cage structure, m16b peptidase, metallopeptidase, peptidasome, protease, hydrolase
• Biological source: Bacillus halodurans C-125; More
• Total number of polymer chains: 4
• Total formula weight: 98318.30

Authors

Aleshin, A.,Gramatikova, S.,Strongin, A.Y.,Stec, B.,Liddington, R.C.,Smith, J.W. (deposition date: 2009-05-07, release date: 2009-12-08, Last modification date: 2023-09-06)

Primary citation

Aleshin, A.E.,Gramatikova, S.,Hura, G.L.,Bobkov, A.,Strongin, A.Y.,Stec, B.,Tainer, J.A.,Liddington, R.C.,Smith, J.W.
Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case.
Structure, 17:1465-1475, 2009

PubMed Abstract: 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.

PubMed: 19913481
DOI: 10.1016/j.str.2009.09.009

Experimental method

X-RAY DIFFRACTION (2.7 Å)