5NA8

Structure of DPP III from Bacteroides thetaiotaomicron in closed form

Summary for 5NA8

• Entry DOI: 10.2210/pdb5na8/pdb
• Descriptor: Putative dipeptidyl-peptidase III, ZINC ION, SULFATE ION (3 entities in total)
• Functional Keywords: bacteroides thetaiotaomicron, metallopeptidase, dipeptidyl peptidase iii, zinc-hydrolase, closed form, hydrolase
• Biological source: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
• Total number of polymer chains: 2
• Total formula weight: 155890.15

Authors

Sabljic, I.,Luic, M. (deposition date: 2017-02-27, release date: 2017-11-15, Last modification date: 2024-01-17)

Primary citation

Sabljic, I.,Mestrovic, N.,Vukelic, B.,Macheroux, P.,Gruber, K.,Luic, M.,Abramic, M.
Crystal structure of dipeptidyl peptidase III from the human gut symbiont Bacteroides thetaiotaomicron.
PLoS ONE, 12:e0187295-e0187295, 2017

PubMed Abstract: Bacteroides thetaiotaomicron is a dominant member of the human intestinal microbiome. The genome of this anaerobe encodes more than 100 proteolytic enzymes, the majority of which have not been characterized. In the present study, we have produced and purified recombinant dipeptidyl peptidase III (DPP III) from B. thetaiotaomicron for the purposes of biochemical and structural investigations. DPP III is a cytosolic zinc-metallopeptidase of the M49 family, involved in protein metabolism. The biochemical results for B. thetaiotaomicron DPP III from our research showed both some similarities to, as well as certain differences from, previously characterised yeast and human DPP III. The 3D-structure of B. thetaiotaomicron DPP III was determined by X-ray crystallography and revealed a two-domain protein. The ligand-free structure (refined to 2.4 Å) was in the open conformation, while in the presence of the hydroxamate inhibitor Tyr-Phe-NHOH, the closed form (refined to 3.3 Å) was observed. Compared to the closed form, the two domains of the open form are rotated away from each other by about 28 degrees. A comparison of the crystal structure of B. thetaiotaomicron DPP III with that of the human and yeast enzymes revealed a similar overall fold. However, a significant difference with functional implications was discovered in the upper domain, farther away from the catalytic centre. In addition, our data indicate that large protein flexibility might be conserved in the M49 family.

PubMed: 29095893
DOI: 10.1371/journal.pone.0187295

Experimental method

X-RAY DIFFRACTION (3.29 Å)