6I7W | pdb_00006i7w

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

• PDB DOI: https://doi.org/10.2210/pdb6I7W/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-19 Released: 2019-01-23 
• Deposition Author(s): Morera, S., Vigouroux, A., El Sahili, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

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

• PubMed: 30632589 
• DOI: https://doi.org/10.1039/c8ob03086c
• Primary Citation 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.

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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. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.87 kDa 
• Atom Count: 4,342 
• Modeled Residue Count: 492 
• Deposited Residue Count: 499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter, substrate binding protein (Agrocinopines A and B)	A	499	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: accA, Atu6139
UniProt
Find proteins for Q52012 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q52012  Go to UniProtKB:  Q52012

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H6Q	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
H6Z	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
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.32	α = 90
b = 108.28	β = 90
c = 113.62	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Morera, S., Vigouroux, A., El Sahili, A.

Revision History  

• 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