6HLZ

Structure in C2 form of the PBP AgtB from A.tumefacien R10 in complex with agropinic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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This is version 1.2 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: https://doi.org/10.1042/BCJ20180861
  • Primary Citation of Related Structures:  
    6HLX, 6HLY, 6HLZ, 6HM2

  • 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. 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.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Agropine permease
A, B
341Agrobacterium tumefaciens LBA4213 (Ach5)Mutation(s): 0 
Gene Names: agtB, X971_5368
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G9Z
Query on G9Z
Download Ideal Coordinates CCD File 
HA [auth A],
LB [auth B]		agropinic acid
C11 H17 N O8
WYIHPABVKQQJFB-SZWOQXJISA-N
P6G
Query on P6G
Download Ideal Coordinates CCD File 
RA [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
P4G
Query on P4G
Download Ideal Coordinates CCD File 
EA [auth A]
FA [auth A]
GA [auth A]
IB [auth B]
JB [auth B]
EA [auth A],
FA [auth A],
GA [auth A],
IB [auth B],
JB [auth B],
KB [auth B]
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
PEG
Query on PEG
Download Ideal Coordinates CCD File 
IA [auth A]
JA [auth A]
KA [auth A]
LA [auth A]
MA [auth A]
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
MB [auth B],
NA [auth A],
NB [auth B],
OA [auth A],
OB [auth B],
PA [auth A],
PB [auth B],
QA [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
BA [auth A]
BB [auth B]
C [auth A]
AA [auth A],
AB [auth B],
BA [auth A],
BB [auth B],
C [auth A],
CA [auth A],
CB [auth B],
D [auth A],
DA [auth A],
DB [auth B],
E [auth A],
EB [auth B],
F [auth A],
FB [auth B],
G [auth A],
GB [auth B],
H [auth A],
HB [auth B],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
WA [auth B],
X [auth A],
XA [auth B],
Y [auth A],
YA [auth B],
Z [auth A],
ZA [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.83α = 90
b = 40.93β = 115.07
c = 117.42γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description