3SG0

The crystal structure of an extracellular ligand-binding receptor from Rhodopseudomonas palustris HaA2

DOI: 10.2210/pdb3SG0/pdb

Classification: SIGNALING PROTEIN
Organism(s): Rhodopseudomonas palustris HaA2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-06-14 Released: 2011-06-29
Deposition Author(s): Tan, K., Mack, J.C., Zerbs, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.162
R-Value Work: 0.150
R-Value Observed: 0.150

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 23606130 Search on PubMedSearch on PubMed Central
DOI: 10.1002/prot.24305
Primary Citation of Related Structures:
4I1D, 3UK0, 3UKJ, 3RPW, 3TX6, 4DQD, 3SG0, 4F8J, 4EYQ, 4EYO

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) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular ligand-binding receptor	A	386	Rhodopseudomonas palustris HaA2	Mutation(s): 0 Gene Names: Rhodopseudomonas palustris, RPB_4630
Find proteins for Q2IR47 (Rhodopseudomonas palustris (strain HaA2)) Explore Q2IR47 Go to UniProtKB: Q2IR47
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
173 Query on 173 Download Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	BENZOYL-FORMIC ACID C₈ H₆ O₃ FAQJJMHZNSSFSM-UHFFFAOYSA-N		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.162
R-Value Work: 0.150
R-Value Observed: 0.150
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.494	α = 90
b = 70.301	β = 90
c = 98.265	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing