6HLZ | pdb_00006hlz

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

• PDB DOI: https://doi.org/10.2210/pdb6HLZ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Agrobacterium tumefaciens LBA4213 (Ach5)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-09-11 Released: 2018-12-26 
• Deposition Author(s): Morera, S., Marty, L., Vigouroux, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.254 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

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

• PubMed: 30552142 
• DOI: https://doi.org/10.1042/BCJ20180861
• Primary Citation 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.

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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.
Institut de Chimie des Substances Naturelles, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, F-69622 Villeurbanne, Lyon, France.
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 [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 80.53 kDa 
• Atom Count: 5,870 
• Modeled Residue Count: 632 
• Deposited Residue Count: 682 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agropine permease	A, B	341	Agrobacterium tumefaciens LBA4213 (Ach5)	Mutation(s): 0  Gene Names: agtB, X971_5368

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G9Z	HA [auth A], LB [auth B]	agropinic acid C11 H17 N O8 WYIHPABVKQQJFB-SZWOQXJISA-N
P6G	RA [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
P4G	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	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	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 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.83	α = 90
b = 40.93	β = 115.07
c = 117.42	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: 2018-12-26 
Deposition Author(s): Morera, S., Marty, L., Vigouroux, A.

Revision History  

• 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