4Y04

Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis (Space)

Summary for 4Y04

• Entry DOI: 10.2210/pdb4y04/pdb
• Related: 4XZY 4Y01 4Y02 4Y06
• Descriptor: Peptidase S46, POTASSIUM ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: space, wt, hydrolase
• Biological source: Porphyromonas gingivalis
• Total number of polymer chains: 1
• Total formula weight: 82216.49

Authors

Sakamoto, Y.,Suzuki, Y.,Iizuka, I.,Tateoka, C.,Roppongi, S.,Fujimoto, M.,Inaka, K.,Tanaka, H.,Yamada, M.,Ohta, K.,Nonaka, T.,Ogasawara, W.,Tanaka, N. (deposition date: 2015-02-05, release date: 2015-07-15, Last modification date: 2024-10-30)

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

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: 26057589
DOI: 10.1038/srep11151

Experimental method

X-RAY DIFFRACTION (1.66 Å)