RCSB PDB - 4EYQ: Crystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris HaA2 in complex with caffeic acid/3-(4-HYDROXY-PHENYL)PYRUVIC ACID

 4EYQ

Crystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris HaA2 in complex with caffeic acid/3-(4-HYDROXY-PHENYL)PYRUVIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DHCClick on this verticalbar to view detailsBest fitted ENOClick on this verticalbar to view details

This is version 1.5 of the entry. See complete history


Literature

Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-Coumaric acid and related aromatic acids.

Tan, K.Chang, C.Cuff, M.Osipiuk, J.Landorf, E.Mack, J.C.Zerbs, S.Joachimiak, A.Collart, F.R.

(2013) Proteins 81: 1709-1726

  • DOI: https://doi.org/10.1002/prot.24305
  • Primary Citation of Related Structures:  
    3RPW, 3SG0, 3TX6, 3UK0, 3UKJ, 4DQD, 4EYO, 4EYQ, 4F8J, 4FB4, 4I1D

  • PubMed Abstract: 

    Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins.


  • Organizational Affiliation

    Biosciences Division, Argonne National Laboratory, Lemont, Illinois, 60439; The Midwest Center for Structural Genomics, Argonne National Laboratory, Lemont, Illinois, 60439; Structural Biology Center, Argonne National Laboratory, Lemont, Illinois, 60439.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular ligand-binding receptor362Rhodopseudomonas palustris HaA2Mutation(s): 0 
Gene Names: RPB_3575
UniProt
Find proteins for Q2IU40 (Rhodopseudomonas palustris (strain HaA2))
Explore Q2IU40 
Go to UniProtKB:  Q2IU40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2IU40
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.338α = 90
b = 88.338β = 90
c = 209.92γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DHCClick on this verticalbar to view detailsBest fitted ENOClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2013-05-15
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Database references
  • Version 1.3: 2013-08-07
    Changes: Database references
  • Version 1.4: 2013-09-25
    Changes: Database references
  • Version 1.5: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary