4ZED
PBP AccA from A. tumefaciens C58 in complex with agrocinopine-3'-O-benzoate
Summary for 4ZED
| Entry DOI | 10.2210/pdb4zed/pdb |
| Related | 4RA1 4ZE8 4ZE9 4ZEB 4ZEC |
| Descriptor | ABC transporter, substrate binding protein (Agrocinopines A and B), [(2S,3S,4R,5R)-2,5-bis(hydroxymethyl)-2-[(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-[oxidanyl-[(2R,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-phosphoryl]oxy-oxolan-3-yl] benzoate, 1,2-ETHANEDIOL, ... (4 entities in total) |
| Functional Keywords | pbp, class c, transport protein |
| Biological source | Agrobacterium tumefaciens (strain C58 / ATCC 33970) |
| Total number of polymer chains | 1 |
| Total formula weight | 57898.67 |
| Authors | El Sahili, A.,Morera, S. (deposition date: 2015-04-20, release date: 2015-08-19, Last modification date: 2024-05-08) |
| Primary citation | El Sahili, A.,Li, S.Z.,Lang, J.,Virus, C.,Planamente, S.,Ahmar, M.,Guimaraes, B.G.,Aumont-Nicaise, M.,Vigouroux, A.,Soulere, L.,Reader, J.,Queneau, Y.,Faure, D.,Morera, S. A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens. Plos Pathog., 11:e1005071-e1005071, 2015 Cited by PubMed Abstract: Periplasmic binding proteins (PBPs) in association with ABC transporters select and import a wide variety of ligands into bacterial cytoplasm. They can also take up toxic molecules, as observed in the case of the phytopathogen Agrobacterium tumefaciens strain C58. This organism contains a PBP called AccA that mediates the import of the antibiotic agrocin 84, as well as the opine agrocinopine A that acts as both a nutrient and a signalling molecule for the dissemination of virulence genes through quorum-sensing. Here, we characterized the binding mode of AccA using purified agrocin 84 and synthetic agrocinopine A by X-ray crystallography at very high resolution and performed affinity measurements. Structural and affinity analyses revealed that AccA recognizes an uncommon and specific motif, a pyranose-2-phosphate moiety which is present in both imported molecules via the L-arabinopyranose moiety in agrocinopine A and the D-glucopyranose moiety in agrocin 84. We hypothesized that AccA is a gateway allowing the import of any compound possessing a pyranose-2-phosphate motif at one end. This was structurally and functionally confirmed by experiments using four synthetic compounds: agrocinopine 3'-O-benzoate, L-arabinose-2-isopropylphosphate, L-arabinose-2-phosphate and D-glucose-2-phosphate. By combining affinity measurements and in vivo assays, we demonstrated that both L-arabinose-2-phosphate and D-glucose-2-phosphate, which are the AccF mediated degradation products of agrocinopine A and agrocin 84 respectively, interact with the master transcriptional regulator AccR and activate the quorum-sensing signal synthesis and Ti plasmid transfer in A. tumefaciens C58. Our findings shed light on the role of agrocinopine and antibiotic agrocin 84 on quorum-sensing regulation in A. tumefaciens and reveal how the PBP AccA acts as vehicle for the importation of both molecules by means of a key-recognition motif. It also opens future possibilities for the rational design of antibiotic and anti-virulence compounds against A. tumefaciens or other pathogens possessing similar PBPs. PubMed: 26244338DOI: 10.1371/journal.ppat.1005071 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.75 Å) |
Structure validation
Download full validation report
