4Y06
Crystal structure of the DAP BII (G675R) dipeptide complex
Summary for 4Y06
| Entry DOI | 10.2210/pdb4y06/pdb |
| Related | 4XZY 4Y01 4Y02 4Y04 |
| Descriptor | Dipeptidyl aminopeptidase BII, LEUCINE, GLUTAMIC ACID, ... (6 entities in total) |
| Functional Keywords | hydrolase |
| Biological source | Pseudoxanthomonas mexicana |
| Total number of polymer chains | 2 |
| Total formula weight | 159949.67 |
| Authors | Sakamoto, Y.,Iizuka, I.,Tateoka, C.,Roppongi, S.,Fujimoto, M.,Nonaka, T.,Ogasawara, W.,Tanaka, N. (deposition date: 2015-02-05, release date: 2015-07-15, Last modification date: 2024-11-06) |
| Primary citation | Sakamoto, Y.,Suzuki, Y.,Iizuka, I.,Tateoka, C.,Roppongi, S.,Fujimoto, M.,Inaka, K.,Tanaka, H.,Yamada, M.,Ohta, K.,Gouda, H.,Nonaka, T.,Ogasawara, W.,Tanaka, N. Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity. Sci Rep, 5:11151-11151, 2015 Cited by PubMed Abstract: The dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) belongs to the S46 family of serine peptidases and preferentially cleaves substrates with Asp/Glu at the P1 position. The molecular mechanism underlying the substrate specificity of PgDPP11, however, is unknown. Here, we report the crystal structure of PgDPP11. The enzyme contains a catalytic domain with a typical double β-barrel fold and a recently identified regulatory α-helical domain. Crystal structure analyses, docking studies, and biochemical studies revealed that the side chain of Arg673 in the S1 subsite is essential for recognition of the Asp/Glu side chain at the P1 position of the bound substrate. Because S46 peptidases are not found in mammals and the Arg673 is conserved among DPP11s, we anticipate that DPP11s could be utilised as targets for antibiotics. In addition, the present structure analyses could be useful templates for the design of specific inhibitors of DPP11s from pathogenic organisms. PubMed: 26057589DOI: 10.1038/srep11151 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.18 Å) |
Structure validation
Download full validation report
