5D88
The Structure of the U32 Peptidase Mk0906
Summary for 5D88
| Entry DOI | 10.2210/pdb5d88/pdb |
| Descriptor | Predicted protease of the collagenase family, ZINC ION, ACETATE ION, ... (4 entities in total) |
| Functional Keywords | u32 peptidase, tim barrel, hydrolase |
| Biological source | Methanopyrus kandleri |
| Total number of polymer chains | 1 |
| Total formula weight | 28549.14 |
| Authors | Baumann, U.,Schacherl, M.,Monatda, A.A.M. (deposition date: 2015-08-15, release date: 2015-12-02, Last modification date: 2024-05-08) |
| Primary citation | Schacherl, M.,Montada, A.A.,Brunstein, E.,Baumann, U. The first crystal structure of the peptidase domain of the U32 peptidase family. Acta Crystallogr.,Sect.D, 71:2505-2512, 2015 Cited by PubMed Abstract: The U32 family is a collection of over 2500 annotated peptidases in the MEROPS database with unknown catalytic mechanism. They mainly occur in bacteria and archaea, but a few representatives have also been identified in eukarya. Many of the U32 members have been linked to pathogenicity, such as proteins from Helicobacter and Salmonella. The first crystal structure analysis of a U32 catalytic domain from Methanopyrus kandleri (gene mk0906) reveals a modified (βα)8 TIM-barrel fold with some unique features. The connecting segment between strands β7 and β8 is extended and helix α7 is located on top of the C-terminal end of the barrel body. The protein exhibits a dimeric quaternary structure in which a zinc ion is symmetrically bound by histidine and cysteine side chains from both monomers. These residues reside in conserved sequence motifs. No typical proteolytic motifs are discernible in the three-dimensional structure, and biochemical assays failed to demonstrate proteolytic activity. A tunnel in which an acetate ion is bound is located in the C-terminal part of the β-barrel. Two hydrophobic grooves lead to a tunnel at the C-terminal end of the barrel in which an acetate ion is bound. One of the grooves binds to a Strep-Tag II of another dimer in the crystal lattice. Thus, these grooves may be binding sites for hydrophobic peptides or other ligands. PubMed: 26627657DOI: 10.1107/S1399004715019549 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.66 Å) |
Structure validation
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