4Y9T

CRYSTAL STRUCTURE OF AN ABC TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM AGROBACTERIUM VITIS S4 (Avi_5305, TARGET EFI-511224) WITH BOUND ALPHA-D-GLUCOSAMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.801 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of an ABC transporter solute-binding protein specific for the amino sugars glucosamine and galactosamine.

Yadava, U.Vetting, M.W.Al Obaidi, N.Carter, M.S.Gerlt, J.A.Almo, S.C.

(2016) Acta Crystallogr.,Sect.F 72: 467-472

  • DOI: 10.1107/S2053230X16007500
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The uptake of exogenous solutes by prokaryotes is mediated by transport systems embedded in the plasma membrane. In many cases, a solute-binding protein (SBP) is utilized to bind ligands with high affinity and deliver them to the membrane-bound compo ...

    The uptake of exogenous solutes by prokaryotes is mediated by transport systems embedded in the plasma membrane. In many cases, a solute-binding protein (SBP) is utilized to bind ligands with high affinity and deliver them to the membrane-bound components responsible for translocation into the cytoplasm. In the present study, Avi_5305, an Agrobacterium vitis SBP belonging to Pfam13407, was screened by differential scanning fluorimetry (DSF) and found to be stabilized by D-glucosamine and D-galactosamine. Avi_5305 is the first protein from Pfam13407 shown to be specific for amino sugars, and co-crystallization resulted in structures of Avi_5305 bound to D-glucosamine and D-galactosamine. Typical of Pfam13407, Avi_5305 consists of two α/β domains linked through a hinge region, with the ligand-binding site located in a cleft between the two domains. Comparisons with Escherichia coli ribose-binding protein suggest that a cation-π interaction with Tyr168 provides the specificity for D-glucosamine/D-galactosamine over D-glucose/D-galactose.


    Organizational Affiliation

    Department of Physics, DDU Gorakhpur University, Gorakhpur 273 009, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABC transporter, solute binding protein
A
346Agrobacterium vitis (strain S4 / ATCC BAA-846)Mutation(s): 0 
Find proteins for B9K0Q5 (Agrobacterium vitis (strain S4 / ATCC BAA-846))
Go to UniProtKB:  B9K0Q5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PA1
Query on PA1

Download SDF File 
Download CCD File 
A
2-amino-2-deoxy-alpha-D-glucopyranose
C6 H13 N O5
MSWZFWKMSRAUBD-UKFBFLRUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.801 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.634α = 90.00
b = 63.611β = 90.00
c = 127.394γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM093342

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2016-06-22
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Derived calculations