6I7W

Structure of the periplasmic binding protein (PBP) AccA in complex with 2-glucose-2-O-lactic acid phosphate (G2LP) from Agrobacterium fabrum C58


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Synthesis of a non-natural glucose-2-phosphate ester able to dupe the acc system of Agrobacterium fabrum.

Li, S.Z.Vigouroux, A.Ahmar, M.El Sahili, A.Soulere, L.Sago, L.Cornu, D.Morera, S.Queneau, Y.

(2019) Org Biomol Chem 17: 1090-1096

  • DOI: https://doi.org/10.1039/c8ob03086c
  • Primary Citation of Related Structures:  
    6I7W

  • PubMed Abstract: 

    The first non-natural derivative of the rare d-glucose-2-phosphate (G2P), namely glucose-2-(O-lactic acid phosphate) (G2LP), has been synthesized. When used as sole carbon source, G2LP enables bacterial growth of the plant pathogenic strain Agrobacterium fabrum C58 (formerly referred to as Agrobacterium tumefaciens). X-ray crystallography and affinity measurements investigations reveal that G2LP binds the periplasmic binding protein (PBP) AccA similarly to the natural compounds and with the same affinity. Moreover, enzymatic assays show that it is able to serve as substrate of the phosphodiesterase AccF. The properties found for G2LP demonstrate that the very unusual glucose-2-phosphoryl residue, present in G2LP, can be used as structural feature for designing non-natural systems fully compatible with the Acc cascade of A. fabrum.


  • Organizational Affiliation

    Univ Lyon, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, CNRS, Université Lyon 1, INSA Lyon, CPE Lyon, ICBMS, UMR 5246, Université Claude Bernard, Bâtiment Lederer, 1 Rue Victor Grignard, 69622 Villeurbanne Cedex, France. Yves.queneau@insa-lyon.fr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter, substrate binding protein (Agrocinopines A and B)499Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: accAAtu6139
UniProt
Find proteins for Q52012 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q52012 
Go to UniProtKB:  Q52012
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ52012
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H6Z
Query on H6Z

Download Ideal Coordinates CCD File 
C [auth A]2-O-[(R)-{[(2S)-1,1-dihydroxypropan-2-yl]oxy}(hydroxy)phosphoryl]-alpha-D-glucopyranose
C9 H19 O11 P
SILWFZFNYLTARD-MRXKBSKTSA-N
H6Q
Query on H6Q

Download Ideal Coordinates CCD File 
B [auth A]2-O-[(R)-{[(2S)-1,1-dihydroxypropan-2-yl]oxy}(hydroxy)phosphoryl]-beta-D-glucopyranose
C9 H19 O11 P
SILWFZFNYLTARD-AVLLYLPDSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
H6Q Binding MOAD:  6I7W Kd: 2000 (nM) from 1 assay(s)
H6Z Binding MOAD:  6I7W Kd: 2000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.32α = 90
b = 108.28β = 90
c = 113.62γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description, Structure summary