Crystal structure of Pseudomonas sp. PDC86 substrate-binding protein Aapf in complex with a signaling molecule HEHEAA

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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Structural basis for a bacterial Pip system plant effector recognition protein.

Luo, S.Coutinho, B.G.Dadhwal, P.Oda, Y.Ren, J.Schaefer, A.L.Greenberg, E.P.Harwood, C.S.Tong, L.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2019462118
  • Primary Citation of Related Structures:  
    7KZ8, 7KZ9

  • 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, N -(2-hydroxyethyl)-2-(2-hydroxyethylamino) acetamide (HEHEAA), as a potent effector of PipR-mediated gene regulation in the plant endophyte Pseudomonas 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 Pseudomonas syringae pv tomato DC3000 does not recognize HEHEAA. However, a single amino acid substitution in the presumed effector-binding pocket of the P. syringae SBP converted it to a weak HEHEAA-binding protein. The P. syringae PipR depends on a plant effector for activity, and our findings imply that different PipR-associated SBPs bind different effectors.

  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, NY 10027.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide/nickel transport system substrate-binding protein AapF
A, B
491Pseudomonas sp. PDC86Mutation(s): 0 
Gene Names: AapF
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XN7 (Subject of Investigation/LOI)
Query on XN7

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
C6 H14 N2 O3
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
O [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
I [auth B]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.395α = 97.22
b = 62.576β = 91.65
c = 92.602γ = 89.97
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118093
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD012018

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description