4GLJ

Crystal structure of methylthioadenosine phosphorylase in complex with rhodamine B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an antarctic soil metagenomic library.

Bartasun, P.Cieslinski, H.Bujacz, A.Wierzbicka-Wos, A.Kur, J.

(2013) PLoS One 8: e55697-e55697

  • DOI: 10.1371/journal.pone.0055697
  • Primary Citation of Related Structures:  
    4GLJ, 4GLF

  • PubMed Abstract: 
  • The presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B ...

    The presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified and its UV-VIS absorbance spectrum and emission spectrum were assayed. Simultaneously, the same spectroscopic studies were carried out for rhodamine B in the absence or presence of RSFP protein or native E. coli proteins, respectively. The results of the spectroscopic studies suggested that the fluorescence of E. coli cells expressing rsfp gene under UV illumination is due to the interaction of rhodamine B molecules with the RSFP protein. Finally, this interaction was proved by a crystallographic study and then by site-directed mutagenesis of rsfp gene sequence. The crystal structures of RSFP apo form (1.98 Å) and complex RSFP/RB (1.90 Å) show a trimer of RSFP molecules located on the crystallographic six fold screw axis. The RSFP complex with rhodamine B revealed the binding site for RB, in the pocket located on the interface between symmetry related monomers.


    Organizational Affiliation

    Department of Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RsfPA297uncultured bacteriumMutation(s): 0 
Gene Names: rsfPmtnP
EC: 2.4.2.28
UniProt
Find proteins for C6KFA4 (uncultured bacterium)
Explore C6KFA4 
Go to UniProtKB:  C6KFA4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RHB
Query on RHB

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]N-[9-(2-carboxyphenyl)-6-(diethylamino)-3H-xanthen-3-ylidene]-N-ethylethanaminium
C28 H31 N2 O3
CVAVMIODJQHEEH-UHFFFAOYSA-O
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.26α = 90
b = 80.26β = 90
c = 81.26γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-20
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description