PDBsum entry 6q8h

Antibiotic

PDB id: 6q8h

Contents

Protein chain

114 a.a.

Ligands

DLE-DLE-DLY-DAL-DLE-DLY-DLY-DLE-DAL-DLY-DLY-DTY-DLY ×2

ZDC ×2

NH2 ×2

Metals

_CA ×2

Waters ×177

PDB id:

6q8h

Name:

Antibiotic

Title:

Structure of fucosylated d-antimicrobial peptide sb10 in complex with the fucose-binding lectin pa-iil at 1.707 angstrom resolution

Structure:

Fucose-binding lectin. Chain: a. Synonym: fucose-binding lectin ii (pa-iil),fucose-binding lectin pa- iil. Engineered: yes. Other_details: fucose-binding lectin pa-iil lecb. Sb10. Chain: b, c. Engineered: yes.

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Gene: lecb, c0043_24310, c0044_25260, c0046_23510, caz10_21840, cw299_25270, di492_13230, dt376_00595, paerug_e15_london_28_01_14_00983, pamh19_1713, rw109_rw109_02453. Expressed in: escherichia coli 'bl21-gold(de3)plyss ag'. Expression_system_taxid: 866768. Synthetic: yes. Synthetic construct.

Resolution:

1.71Å R-factor: 0.169 R-free: 0.189

Authors:

S.Baeriswyl,A.Stocker,J.L.Reymond

Key ref:

S.Baeriswyl et al. (2019). X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes. ACS Chem Biol, 14, 758-766. PubMed id: 30830745 DOI: 10.1021/acschembio.9b00047

Date:

14-Dec-18 Release date: 20-Mar-19

Protein chain

Q9HYN5  (Q9HYN5_PSEAE) -  Fucose-binding lectin PA-IIL from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 115 a.a.

Struc: 114 a.a.

DOI no: 10.1021/acschembio.9b00047

ACS Chem Biol 14:758-766 (2019)

PubMed id: 30830745

X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.

S.Baeriswyl, B.H.Gan, T.N.Siriwardena, R.Visini, M.Robadey, S.Javor, A.Stocker, T.Darbre, J.L.Reymond.

ABSTRACT

Herein, we report X-ray crystal structures of 11-13 residue antimicrobial peptides (AMPs) active against Pseudomonas aeruginosa as complexes of fucosylated d-enantiomeric sequences with the P. aeruginosa lectin LecB. These represent the first crystal structures of short AMPs. In 24 individual structures of eight different peptides, we found mostly α-helices assembled as two-helix or four-helix bundles with a hydrophobic core and cationic residues pointing outside. Two of the analogs formed an extended structure engaging in multiple contacts with the lectin. Molecular dynamics (MD) simulations showed that α-helices are stabilized by bundle formation and suggested that the N-terminal acyl group present in the linker to the fucosyl group can extend the helix by one additional H-bond and increase α-helix amphiphilicity. Investigating N-terminal acylation led to AMPs with equivalent and partly stronger antibacterial effects compared to the free peptide.