7KZ8

Crystal structure of substrate-binding protein Aapf from Pseudomonas sp. PDC86

Summary for 7KZ8

• Entry DOI: 10.2210/pdb7kz8/pdb
• Descriptor: Peptide/nickel transport system substrate-binding protein AapF, GLYCEROL (3 entities in total)
• Functional Keywords: substrate-binding protein (sbps), abc-transporter, type-c sbps, transport protein
• Biological source: Pseudomonas sp. PDC86
• Total number of polymer chains: 1
• Total formula weight: 55274.11

Authors

Luo, S.,Dadhwal, P.,Tong, L. (deposition date: 2020-12-10, release date: 2021-03-17, Last modification date: 2023-10-18)

Primary citation

Luo, S.,Coutinho, B.G.,Dadhwal, P.,Oda, Y.,Ren, J.,Schaefer, A.L.,Greenberg, E.P.,Harwood, C.S.,Tong, L.
Structural basis for a bacterial Pip system plant effector recognition protein.
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: A number of plant-associated proteobacteria have LuxR family transcription factors that we refer to as PipR subfamily members. PipR proteins play roles in interactions between bacteria and their plant hosts, and some are important for bacterial virulence of plants. We identified an ethanolamine derivative, -(2-hydroxyethyl)-2-(2-hydroxyethylamino) acetamide (HEHEAA), as a potent effector of PipR-mediated gene regulation in the plant endophyte GM79. HEHEAA-dependent PipR activity requires an ATP-binding cassette-type active transport system, and the periplasmic substrate-binding protein (SBP) of that system binds HEHEAA. To begin to understand the molecular basis of PipR system responses to plant factors we crystallized a HEHEAA-responsive SBP in the free- and HEHEAA-bound forms. The SBP, which is similar to peptide-binding SBPs, was in a closed conformation. A narrow cavity at the interface of its two lobes is wide enough to bind HEHEAA, but it cannot accommodate peptides with side chains. The polar atoms of HEHEAA are recognized by hydrogen-bonding interactions, and additional SBP residues contribute to the binding site. This binding mode was confirmed by a structure-based mutational analysis. We also show that a closely related SBP from the plant pathogen pv DC3000 does not recognize HEHEAA. However, a single amino acid substitution in the presumed effector-binding pocket of the SBP converted it to a weak HEHEAA-binding protein. The PipR depends on a plant effector for activity, and our findings imply that different PipR-associated SBPs bind different effectors.

PubMed: 33649224
DOI: 10.1073/pnas.2019462118

Experimental method

X-RAY DIFFRACTION (2.2 Å)