8CDO

PBP AccA-F144YG440Q from A. tumefaciens Bo542 in complex with agrocinopine C-like


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity.

Morera, S.Vigouroux, A.Aumont-Nicaise, M.Ahmar, M.Meyer, T.El Sahili, A.Deicsics, G.Gonzalez-Mula, A.Li, S.Dore, J.Sirigu, S.Legrand, P.Penot, C.Andre, F.Faure, D.Soulere, L.Queneau, Y.Vial, L.

(2024) Biochem J 481: 93-117

  • DOI: https://doi.org/10.1042/BCJ20230273
  • Primary Citation of Related Structures:  
    8C6R, 8C6U, 8C6W, 8C6Y, 8C75, 8CAW, 8CAY, 8CB9, 8CDO, 8CH1, 8CH2, 8CH3, 8CHC, 8CI6, 8CJU, 8CKD, 8CKE, 8CKO

  • PubMed Abstract: 

    Plants genetically modified by the pathogenic Agrobacterium strain C58 synthesize agrocinopines A and B, whereas those modified by the pathogenic strain Bo542 produce agrocinopines C and D. The four agrocinopines (A, B, C and D) serve as nutrients by agrobacteria and signaling molecule for the dissemination of virulence genes. They share the uncommon pyranose-2-phosphate motif, represented by the l-arabinopyranose moiety in agrocinopines A/B and the d-glucopyranose moiety in agrocinopines C/D, also found in the antibiotic agrocin 84. They are imported into agrobacterial cytoplasm via the Acc transport system, including the solute-binding protein AccA coupled to an ABC transporter. We have previously shown that unexpectedly, AccA from strain C58 (AccAC58) recognizes the pyranose-2-phosphate motif present in all four agrocinopines and agrocin 84, meaning that strain C58 is able to import agrocinopines C/D, originating from the competitor strain Bo542. Here, using agrocinopine derivatives and combining crystallography, affinity and stability measurements, modeling, molecular dynamics, in vitro and vivo assays, we show that AccABo542 and AccAC58 behave differently despite 75% sequence identity and a nearly identical ligand binding site. Indeed, strain Bo542 imports only compounds containing the d-glucopyranose-2-phosphate moiety, and with a lower affinity compared with strain C58. This difference in import efficiency makes C58 more competitive than Bo542 in culture media. We can now explain why Agrobacterium/Allorhizobium vitis strain S4 is insensitive to agrocin 84, although its genome contains a conserved Acc transport system. Overall, our work highlights AccA proteins as a case study, for which stability and dynamics drive specificity.


  • Organizational Affiliation

    Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Agrocinopine utilization periplasmic binding protein AccA498Agrobacterium tumefaciensMutation(s): 2 
Gene Names: accAAgrTiChry5_232
UniProt
Find proteins for A5WYD2 (Rhizobium radiobacter)
Explore A5WYD2 
Go to UniProtKB:  A5WYD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5WYD2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
B, C
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ALX
Query on ALX

Download Ideal Coordinates CCD File 
Q [auth A]2-O-phosphono-alpha-D-glucopyranose
C6 H13 O9 P
SIUIENVKPUKAHD-DVKNGEFBSA-N
BNX (Subject of Investigation/LOI)
Query on BNX

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P [auth A]2-O-phosphono-beta-D-glucopyranose
C6 H13 O9 P
SIUIENVKPUKAHD-VFUOTHLCSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

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O [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

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E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

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F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.116α = 90
b = 122.116β = 90
c = 122.116γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Database references