6HM2

Structure in P1 form of the PBP AgtB in complex with agropinic acid from A.tumefacien R10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for two efficient modes of agropinic acid opine import into the bacterial pathogenAgrobacterium tumefaciens.

Marty, L.Vigouroux, A.Aumont-Nicaise, M.Pelissier, F.Meyer, T.Lavire, C.Dessaux, Y.Morera, S.

(2019) Biochem J 476: 165-178

  • DOI: 10.1042/BCJ20180861
  • Primary Citation of Related Structures:  
    6HLY, 6HLX, 6HM2, 6HLZ

  • PubMed Abstract: 
  • Agrobacterium tumefaciens pathogens genetically modify their host plants to drive the synthesis of opines in plant tumors. The mannityl-opine family encompasses mannopine, mannopinic acid, agropine and agropinic acid. These opines serve as nutrients and are imported into bacteria via periplasmic-binding proteins (PBPs) in association with ABC transporters ...

    Agrobacterium tumefaciens pathogens genetically modify their host plants to drive the synthesis of opines in plant tumors. The mannityl-opine family encompasses mannopine, mannopinic acid, agropine and agropinic acid. These opines serve as nutrients and are imported into bacteria via periplasmic-binding proteins (PBPs) in association with ABC transporters. Structural and affinity data on agropine and agropinic acid opines bound to PBPs are currently lacking. Here, we investigated the molecular basis of AgtB and AgaA, proposed as the specific PBP for agropine and agropinic acid import, respectively. Using genetic approaches and affinity measurements, we identified AgtB and its transporter as responsible for agropine uptake in agropine-assimilating agrobacteria. Nonetheless, we showed that AgtB binds agropinic acid with a higher affinity than agropine, and we structurally characterized the agropinic acid-binding mode through three crystal structures at 1.4, 1.74 and 1.9 Å resolution. In the crystallization time course, obtaining a crystal structure of AgtB with agropine was unsuccessful due to the spontaneous lactamization of agropine into agropinic acid. AgaA binds agropinic acid only with a similar affinity in nanomolar range as AgtB. The structure of AgaA bound to agropinic acid at 1.65 Å resolution defines a different agropinic acid-binding signature. Our work highlights the structural and functional characteristics of two efficient agropinic acid assimilation pathways, of which one is also involved in agropine assimilation.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France solange.morera@i2bc.paris-saclay.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Agropine permeaseA, B, C, D, E341Agrobacterium tumefaciens LBA4213 (Ach5)Mutation(s): 0 
Gene Names: agtBX971_5368
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G9Z (Subject of Investigation/LOI)
Query on G9Z

Download Ideal Coordinates CCD File 
F [auth A], J [auth B], N [auth C], R [auth D], W [auth E]agropinic acid
C11 H17 N O8
WYIHPABVKQQJFB-SZWOQXJISA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , K [auth B] , L [auth B] , O [auth C] , P [auth C] , S [auth D] , T [auth D] , 
G [auth A],  H [auth A],  K [auth B],  L [auth B],  O [auth C],  P [auth C],  S [auth D],  T [auth D],  U [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A], M [auth B], Q [auth C], V [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.57α = 71.14
b = 86.31β = 81
c = 106.52γ = 76.32
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: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references