Structure of the periplasmic binding protein (PBP) NocT from A.tumefaciens C58 in complex with histopine.

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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Structural basis for high specificity of octopine binding in the plant pathogen Agrobacterium tumefaciens.

Vigouroux, A.El Sahili, A.Lang, J.Aumont-Nicaise, M.Dessaux, Y.Faure, D.Morera, S.

(2017) Sci Rep 7: 18033-18033

  • DOI: https://doi.org/10.1038/s41598-017-18243-8
  • Primary Citation of Related Structures:  
    5ORE, 5ORG, 5OT8, 5OT9, 5OTA, 5OTC

  • PubMed Abstract: 

    Agrobacterium pathogens of octopine- and nopaline-types force host plants to produce either octopine or nopaline compounds, which they use as nutrients. Two Agrobacterium ABC-transporters and their cognate periplasmic binding proteins (PBPs) OccJ and NocT import octopine and nopaline/octopine, respectively. Here, we show that both octopine transport and degradation confer a selective advantage to octopine-type A. tumefaciens when it colonizes plants. We report the X-ray structures of the unliganded PBP OccJ and its complex with octopine as well as a structural comparison with NocT and the related PBP LAO from Salmonella enterica, which binds amino acids (lysine, arginine and ornithine). We investigated the specificity of OccJ, NocT and LAO using several ligands such as amino acids, octopine, nopaline and octopine analogues. OccJ displays a high selectivity and nanomolar range affinity for octopine. Altogether, the structural and affinity data allowed to define an octopine binding signature in PBPs and to construct a OccJ mutant impaired in octopine binding, a selective octopine-binding NocT and a non-selective octopine-binding LAO by changing one single residue in these PBPs. We proposed the PBP OccJ as a major trait in the ecological specialization of octopine-type Agrobacterium pathogens when they colonize and exploit the plant host.

  • Organizational Affiliation

    NTU Institute for Structural Biology, Nanyang Technological University, Experimental Medicine Building, Singapore, 636921, Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nopaline-binding periplasmic protein
A, B
265Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: nocTAtu6027AGR_pTi_67
Find proteins for P35120 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore P35120 
Go to UniProtKB:  P35120
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35120
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.81α = 90
b = 113.81β = 90
c = 37.85γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-03
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection