Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers.

Buth, S.A.; Shneider, M.M.; Scholl, D.; Leiman, P.G.

doi:10.2210/pdb6cl5/pdb

Macromolecule Content

Total Structure Weight: 244769.92
Atom Count: 16858
Residue Count: 2304
Unique protein chains: 1

6CL5

Structure of P. aeruginosa R1 pyocin fiber PALES_06171 comprising C-terminal residues 323-701

DOI: 10.2210/pdb6CL5/pdb

Classification: VIRAL PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli

Deposited: 2018-03-01 Released: 2018-06-27
Deposition Author(s): Buth, S.A., Shneider, M.M., Leiman, P.G.
Funding Organization(s): SNSF; EPFL running cost grant

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.324 Å
R-Value Free: 0.206
R-Value Work: 0.169

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers.

Buth, S.A., Shneider, M.M., Scholl, D., Leiman, P.G.

(2018) Viruses 10: --

PubMed: 30110933 Search on PubMedSearch on PubMed Central
DOI: 10.3390/v10080427

PubMed Abstract:

The R-type pyocins are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. Structurally, the R-type pyocins are similar to "simple" contractile tails, such as those of phage P2 and Mu. The pyocin recognizes and binds to its target with the help of fibers that emanate from the baseplate structure at one end of the particle. Subsequently, the pyocin contracts its sheath and drives the rigid tube through the host cell envelope. This causes depolarization of the cytoplasmic membrane and cell death. The host cell surface-binding fiber is ~340 Å-long and is attached to the baseplate with its N-terminal domain. Here, we report the crystal structures of C-terminal fragments of the R1 and R2 pyocin fibers that comprise the distal, receptor-binding part of the protein. Both proteins are ~240 Å-long homotrimers in which slender rod-like domains are interspersed with more globular domains-two tandem knob domains in the N-terminal part of the fragment and a lectin-like domain at its C-terminus. The putative substrate binding sites are separated by about 100 Å, suggesting that binding of the fiber to the cell surface causes the fiber to adopt a certain orientation relative to the baseplate and this then triggers sheath contraction.

Organizational Affiliation:

Institute of Physics of Biologic Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, 1015 Lausanne, Switzerland. mm_shn@mail.ru.,Institute of Physics of Biologic Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, 1015 Lausanne, Switzerland. pgleiman@utmb.edu.,Pylum Biosciences, 385 Oyster Point Blvd., Suite 6A, South San Francisco, CA 94080, USA. dean@avidbiotics.com.,Institute of Physics of Biologic Systems, École Polytechnique Fédérale de Lausanne (EPFL), BSP-415, 1015 Lausanne, Switzerland. sebuth@utmb.edu.,Shemyakin Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Mikluho Maklaya Str., Moscow 117997, Russia. mm_shn@mail.ru.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tail fiber protein	A, B, C, D, E, F	384	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: HR1
Find proteins for Q9KW03 (Pseudomonas aeruginosa) Go to UniProtKB: Q9KW03
Protein Feature View Full Protein Feature View for Q9KW03

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
NA Query on NA Download SDF File Download CCD File	A, B, C, D, E, F	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download SDF File Download CCD File	A, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction
FE Query on FE Download SDF File Download CCD File	A, D	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Ligand Interaction