PDBsum entry 5wdl

Hydrolase

PDB id: 5wdl

Contents

Protein chains

(+ 0 more) 372 a.a.

Ligands

R33 ×6

Metals

__K ×12

Waters ×780

PDB id:

5wdl

Name:

Hydrolase

Title:

A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium p. Distasonis

Structure:

AminopeptidasE C. Chain: a, b, c, d, e, f. Fragment: unp residues 33-405. Engineered: yes

Source:

Parabacteroides distasonis (strain atcc 8503 / dsm 20701 / cip 104284 / jcm 5825 / nctc 11152). Organism_taxid: 435591. Strain: atcc 8503 / dsm 20701 / cip 104284 / jcm 5825 / nctc 11152. Gene: bdi_2249. Expressed in: escherichia coli 'bl21-gold(de3)plyss ag'. Expression_system_taxid: 866768

Resolution:

2.63Å R-factor: 0.173 R-free: 0.212

Authors:

D.W.Wolan,J.H.Xu,A.Solania,S.Chatterjee,Z.Jiang,A.J.Odonoghue

Key ref:

J.H.Xu et al. (2018). A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro. ACS Chem Biol, 13, 2513-2521. PubMed id: 30085657 DOI: 10.1021/acschembio.8b00420

Date:

05-Jul-17 Release date: 11-Jul-18

Protein chains

A6LE66  (A6LE66_PARD8) -  Aminopeptidase from Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)

Seq: 405 a.a.

Struc: 372 a.a.

DOI no: 10.1021/acschembio.8b00420

ACS Chem Biol 13:2513-2521 (2018)

PubMed id: 30085657

A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro.

J.H.Xu, Z.Jiang, A.Solania, S.Chatterjee, B.Suzuki, C.B.Lietz, V.Y.H.Hook, A.J.O'Donoghue, D.W.Wolan.

ABSTRACT

Proteases within the C1B hydrolase family are encoded by many organisms. We subjected a putative C1B-like cysteine protease secreted by the human gut commensal Parabacteroides distasonis to mass spectrometry-based substrate profiling to find preferred peptide substrates. The P. distasonis protease, which we termed Pd_dinase, has a sequential diaminopeptidase activity with strong specificity for N-terminal glycine residues. Using the substrate sequence information, we verified the importance of the P2 glycine residue with a panel of fluorogenic substrates and calculated k_cat and K_M for the dipeptide glycine-arginine-AMC. A potent and irreversible dipeptide inhibitor with a C-terminal acyloxymethyl ketone warhead, glycine-arginine- AOMK, was then synthesized and demonstrated that the Pd_dinase active site requires a free N-terminal amine for potent and rapid inhibition. We next determined the homohexameric Pd_dinase structure in complex with glycine-arginine- AOMK and uncovered unexpected active site features that govern the strict substrate preferences and differentiate this protease from members of the C1B and broader papain-like C1 protease families. We finally showed that Pd_dinase hydrolyzes several human antimicrobial peptides and therefore posit that this P. distasonis enzyme may be secreted into the extracellular milieu to assist in gut colonization by inactivation of host antimicrobial peptides.