6EPZ

Structure of the periplasmic binding protein MelB (Atu4661) in complex with melibiose from Agrobacterium fabrum C58

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history. 


Literature

The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogenAgrobacterium fabrum.

Meyer, T., Vigouroux, A., Aumont-Nicaise, M., Comte, G., Vial, L., Lavire, C., Morera, S.

(2018) J Biol Chem 293: 7930-7941

  • DOI: https://doi.org/10.1074/jbc.RA118.001856
  • Primary Citation of Related Structures:  
    6EPY, 6EPZ, 6EQ0, 6EQ1, 6EQ8

  • PubMed Abstract: 

    The bacterial plant pathogen Agrobacterium fabrum uses periplasmic-binding proteins (PBPs) along with ABC transporters to import a wide variety of plant molecules as nutrients. Nonetheless, how A. fabrum acquires plant metabolites is incompletely understood. Using genetic approaches and affinity measurements, we identified here the PBP MelB and its transporter as being responsible for the uptake of the raffinose family of oligosaccharides (RFO), which are the most widespread d-galactose-containing oligosaccharides in higher plants. We also found that the RFO precursor galactinol, recently described as a plant defense molecule, is imported into Agrobacterium via MelB with nanomolar range affinity. Structural analyses and binding mode comparisons of the X-ray structures of MelB in complex with raffinose, stachyose, galactinol, galactose, and melibiose (a raffinose degradation product) revealed how MelB recognizes the nonreducing end galactose common to all these ligands and that MelB has a strong preference for a two-unit sugar ligand. Of note, MelB conferred a competitive advantage to A. fabrum in colonizing the rhizosphere of tomato plants. Our integrative work highlights the structural and functional characteristics of melibiose and galactinol assimilation by A. fabrum , leading to a competitive advantage for these bacteria in the rhizosphere. We propose that the PBP MelB, which is highly conserved among both symbionts and pathogens from Rhizobiace family, is a major trait in these bacteria required for early steps of plant colonization.

    • Organizational Affiliation: 

    UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, F-69622, Villeurbanne, Lyon, France.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic alpha-galactoside-binding proteinA,
B [auth D],
C,
D [auth B]		683Agrobacterium tumefaciensMutation(s): 0 
Gene Names: SY94_4618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose
E, F, G, H
2N/A
Glycosylation Resources
GlyTouCan:  G54976AD
GlyCosmos:  G54976AD
GlyGen:  G54976AD
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
BA [auth D]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO
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EA [auth C]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
EA [auth C],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
PA [auth B],
QA [auth B],
U [auth D],
V [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL
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AA [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
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CA [auth C],
DA [auth C],
I [auth A],
OA [auth B],
T [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
FA [auth C]
GA [auth C]
HA [auth C]
IA [auth C]
JA [auth C]
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
TA [auth B],
UA [auth B],
VA [auth B],
W [auth D],
WA [auth B],
X [auth D],
XA [auth B],
Y [auth D],
YA [auth B],
Z [auth D],
ZA [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 351.61α = 90
b = 73.73β = 105.38
c = 107.58γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
FFTphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
CNRSFranceMI

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-06-06
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-13
    Changes: Structure summary