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Structure paper

TitleA highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity.
Journal, issue, pagesBiochem. J., Vol. 481, Page 93-117, Year 2024
Publish dateJan 12, 2023 (structure data deposition date)
AuthorsMorera, S. / Vigouroux, A. / Aumont-Nicaise, M. / Ahmar, M. / Meyer, T. / El Sahili, A. / Deicsics, G. / Gonzalez-Mula, A. / Li, S. / Dore, J. ...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.
External linksBiochem. J. / PubMed:38058289
MethodsX-ray diffraction
Resolution1.199 - 2.8 Å
Structure data

PDB-8c6r:
PBP AccA from A. tumefaciens Bo542 in apoform 4
Method: X-RAY DIFFRACTION / Resolution: 1.884 Å

PDB-8c6u:
PBP AccA-G145YG440Q mutant from A. tumefaciens Bo542 in apoform 4
Method: X-RAY DIFFRACTION / Resolution: 1.843 Å

PDB-8c6w:
PBP AccA from A. tumefaciens Bo542 in apoform 1
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-8c6y:
PBP AccA from A. tumefaciens Bo542 in apoform 2
Method: X-RAY DIFFRACTION / Resolution: 1.901 Å

PDB-8c75:
PBP AccA from A. tumefaciens Bo542 in apoform 3
Method: X-RAY DIFFRACTION / Resolution: 1.673 Å

PDB-8caw:
PBP AccA from A. tumefaciens Bo542 in complex with agrocin84
Method: X-RAY DIFFRACTION / Resolution: 1.256 Å

PDB-8cay:
PBP AccA from A. tumefaciens Bo542 in complex with Agrocinopine D-like
Method: X-RAY DIFFRACTION / Resolution: 1.626 Å

PDB-8cb9:
PBP AccA from A. tumefaciens Bo542 in complex with D-Glucose-2-phosphate
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-8cdo:
PBP AccA-F144YG440Q from A. tumefaciens Bo542 in complex with agrocinopine C-like
Method: X-RAY DIFFRACTION / Resolution: 1.32 Å

PDB-8ch1:
PBP AccA from A. vitis S4 in complex with Agrocinopine A
Method: X-RAY DIFFRACTION / Resolution: 1.496 Å

PDB-8ch2:
PBP AccA from A. vitis S4 in complex with L-arabinose-2-phosphate (A2P)
Method: X-RAY DIFFRACTION / Resolution: 1.404 Å

PDB-8ch3:
PBP AccA from A. vitis S4 in complex with Agrocinopine C-like
Method: X-RAY DIFFRACTION / Resolution: 1.398 Å

PDB-8chc:
PBP AccA from A. vitis S4 in complex with Agrocinopine D-like
Method: X-RAY DIFFRACTION / Resolution: 1.679 Å

PDB-8ci6:
PBP AccA from A. vitis S4 in complex with D-glucose-2-phosphate (G2P)
Method: X-RAY DIFFRACTION / Resolution: 1.199 Å

PDB-8cju:
PBP AccA from A. vitis S4 in complex with agrocin84
Method: X-RAY DIFFRACTION / Resolution: 1.349 Å

PDB-8ckd:
PBP AccA from A. fabrum C58 in complex with agrocinopine D-like
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-8cke:
PBP AccA from A.tumefaciens C58 in complex with agrocinopine A in space group I222
Method: X-RAY DIFFRACTION / Resolution: 1.298 Å

PDB-8cko:
PBP AccA from A.tumefaciens C58 in complex with agrocinopine C-like
Method: X-RAY DIFFRACTION / Resolution: 1.421 Å

Chemicals

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-EDO:
1,2-ETHANEDIOL

ChemComp-PGE:
TRIETHYLENE GLYCOL

ChemComp-HOH:
WATER

ChemComp-ACT:
ACETATE ION

ChemComp-NA:
Unknown entry

ChemComp-C84:
[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-N-[9-[(2R,3S,5R)-5-[[[(2R,3S)-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid

ChemComp-UKU:
[(2S,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-N-[9-[(2R,3S,5R)-5-[[[(2R,3S)-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid

ChemComp-Y4H:
Agrocinopine D-like (C2-C2 linked; with an alpha and beta-D-glucopyranose)

ChemComp-Y45:
Agrocinopine D-like (C2-C2 linked; with two alpha-D-glucopyranoses)

ChemComp-BNX:
2-O-phosphono-beta-D-glucopyranose

ChemComp-ALX:
2-O-phosphono-alpha-D-glucopyranose

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM

ChemComp-VDF:
2-O-phosphono-beta-L-arabinopyranose

ChemComp-LAO:
2-O-phosphono-alpha-L-arabinopyranose

Source
  • agrobacterium tumefaciens (bacteria)
  • agrobacterium vitis s4 (bacteria)
  • allorhizobium ampelinum s4 (bacteria)
  • agrobacterium fabrum str. c58 (bacteria)
KeywordsTRANSPORT PROTEIN / a Periplasmic binding protein / a solute binding protein / Periplasmic binding protein / solute binding protein

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