4JB0

Rhodopseudomonas palustris (strain CGA009) Rp1789 transport protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The CouPSTU and TarPQM Transporters in Rhodopseudomonas palustris: Redundant, Promiscuous Uptake Systems for Lignin-Derived Aromatic Substrates.

Salmon, R.C.Cliff, M.J.Rafferty, J.B.Kelly, D.J.

(2013) Plos One 8: e59844-e59844

  • DOI: 10.1371/journal.pone.0059844
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biodegradation of lignin, one of the most abundant carbon compounds on Earth, has important biotechnological applications in the derivation of useful products from lignocellulosic wastes. The purple photosynthetic bacterium Rhodopseudomonas palus ...

    The biodegradation of lignin, one of the most abundant carbon compounds on Earth, has important biotechnological applications in the derivation of useful products from lignocellulosic wastes. The purple photosynthetic bacterium Rhodopseudomonas palustris is able to grow photoheterotrophically under anaerobic conditions on a range of phenylpropeneoid lignin monomers, including coumarate, ferulate, caffeate, and cinnamate. RPA1789 (CouP) is the periplasmic binding-protein component of an ABC system (CouPSTU; RPA1789, RPA1791-1793), which has previously been implicated in the active transport of this class of aromatic substrate. Here, we show using both intrinsic tryptophan fluorescence and isothermal titration calorimetry that CouP binds a range of phenylpropeneoid ligands with K d values in the nanomolar range. The crystal structure of CouP with ferulate as the bound ligand shows H-bond interactions between the 4-OH group of the aromatic ring with His309 and Gln305. H-bonds are also made between the carboxyl group on the ferulate side chain and Arg197, Ser222, and Thr102. An additional transport system (TarPQM; RPA1782-1784), a member of the tripartite ATP-independent periplasmic (TRAP) transporter family, is encoded at the same locus as rpa1789 and several other genes involved in coumarate metabolism. We show that the periplasmic binding-protein of this system (TarP; RPA1782) also binds coumarate, ferulate, caffeate, and cinnamate with nanomolar K d values. Thus, we conclude that R. palustris uses two redundant but energetically distinct primary and secondary transporters that both employ high-affinity periplasmic binding-proteins to maximise the uptake of lignin-derived aromatic substrates from the environment. Our data provide a detailed thermodynamic and structural basis for understanding the interaction of lignin-derived aromatic substrates with proteins and will be of use in the further exploitation of the flexible metabolism of R. palustris for anaerobic aromatic biotransformations.


    Organizational Affiliation

    Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
branched-chain amino acid transport system substrate-binding protein
A
370Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)Mutation(s): 0 
Find proteins for Q6N8W4 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Go to UniProtKB:  Q6N8W4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ENO
Query on ENO

Download SDF File 
Download CCD File 
A
3-(4-HYDROXY-PHENYL)PYRUVIC ACID
HPP
C9 H8 O4
KKADPXVIOXHVKN-UHFFFAOYSA-N
 Ligand Interaction
FER
Query on FER

Download SDF File 
Download CCD File 
A
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
FERULIC ACID
C10 H10 O4
KSEBMYQBYZTDHS-HWKANZROSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.970α = 90.00
b = 70.740β = 90.00
c = 105.300γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-02-19 
  • Released Date: 2013-04-17 
  • Deposition Author(s): Salmon, R.

Revision History 

  • Version 1.0: 2013-04-17
    Type: Initial release