4F06

Crystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris HaA2 RPB_2270 in complex with P-HYDROXYBENZOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.122 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins.

Michalska, K.Chang, C.Mack, J.C.Zerbs, S.Joachimiak, A.Collart, F.R.

(2012) J.Mol.Biol. 423: 555-575

  • DOI: 10.1016/j.jmb.2012.08.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In vitro growth experiments have demonstrated that aromatic compounds derived from lignin can be metabolized and represent a major carbon resource for many soil bacteria. However, the proteins that mediate the movement of these metabolites across the ...

    In vitro growth experiments have demonstrated that aromatic compounds derived from lignin can be metabolized and represent a major carbon resource for many soil bacteria. However, the proteins that mediate the movement of these metabolites across the cell membrane have not been thoroughly characterized. To address this deficiency, we used a library representative of lignin degradation products and a thermal stability screen to determine ligand specificity for a set of solute-binding proteins (SBPs) from ATP-binding cassette (ABC) transporters. The ligand mapping process identified a set of proteins from Alphaproteobacteria that recognize various benzoate derivatives. Seven high-resolution crystal structures of these proteins in complex with four different aromatic compounds were obtained. The protein-ligand complexes provide details of molecular recognition that can be used to infer binding specificity. This structure-function characterization provides new insight for the biological roles of these ABC transporters and their SBPs, which had been previously annotated as branched-chain amino-acid-binding proteins. The knowledge derived from the crystal structures provides a foundation for development of sequence-based methods to predict the ligand specificity of other uncharacterized transporters. These results also demonstrate that Alphaproteobacteria possess a diverse set of transport capabilities for lignin-derived compounds. Characterization of this new class of transporters improves genomic annotation projects and provides insight into the metabolic potential of soil bacteria.


    Organizational Affiliation

    Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Extracellular ligand-binding receptor
A
371Rhodopseudomonas palustris (strain HaA2)Mutation(s): 0 
Find proteins for Q2IXT5 (Rhodopseudomonas palustris (strain HaA2))
Go to UniProtKB:  Q2IXT5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PHB
Query on PHB

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Download CCD File 
A
P-HYDROXYBENZOIC ACID
C7 H6 O3
FJKROLUGYXJWQN-UHFFFAOYSA-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

Unit Cell:
Length (Å)Angle (°)
a = 42.135α = 90.00
b = 61.174β = 90.00
c = 130.177γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-3000data scaling
REFMACrefinement
MLPHAREphasing
ARP/wARPmodel building
SHELXDEphasing
SBC-Collectdata collection
Cootmodel building
RESOLVEphasing
HKL-3000phasing
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-09-12
    Type: Database references
  • Version 1.2: 2012-10-24
    Type: Database references