7QZ7

Transcriptional regulator LmrR with bound daunomycin and with Trp-67 and Trp-96 replaced by 5,6,7-trifluoroTrp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

The Role of Tryptophan in pi Interactions in Proteins: An Experimental Approach.

Shao, J.Kuiper, B.P.Thunnissen, A.W.H.Cool, R.H.Zhou, L.Huang, C.Dijkstra, B.W.Broos, J.

(2022) J Am Chem Soc 144: 13815-13822

  • DOI: 10.1021/jacs.2c04986
  • Primary Citation of Related Structures:  
    7QZ5, 7QZ6, 7QZ7, 7QZ8, 7QZ9

  • PubMed Abstract: 
  • In proteins, the amino acids Phe, Tyr, and especially Trp are frequently involved in π interactions such as π-π, cation-π, and CH-π bonds. These interactions are often crucial for protein structure and protein-ligand binding. A powerful means to study these interactions is progressive fluorination of these aromatic residues to modulate the electrostatic component of the interaction ...

    In proteins, the amino acids Phe, Tyr, and especially Trp are frequently involved in π interactions such as π-π, cation-π, and CH-π bonds. These interactions are often crucial for protein structure and protein-ligand binding. A powerful means to study these interactions is progressive fluorination of these aromatic residues to modulate the electrostatic component of the interaction. However, to date no protein expression platform is available to produce milligram amounts of proteins labeled with such fluorinated amino acids. Here, we present a Lactococcus lactis Trp auxotroph-based expression system for efficient incorporation (≥95%) of mono-, di-, tri-, and tetrafluorinated, as well as a methylated Trp analog. As a model protein we have chosen LmrR, a dimeric multidrug transcriptional repressor protein from L. lactis. LmrR binds aromatic drugs, like daunomycin and riboflavin, between Trp96 and Trp96' in the dimer interface. Progressive fluorination of Trp96 decreased the affinity for the drugs 6- to 70-fold, clearly establishing the importance of electrostatic π-π interactions for drug binding. Presteady state kinetic data of the LmrR-drug interaction support the enthalpic nature of the interaction, while high resolution crystal structures of the labeled protein-drug complexes provide for the first time a structural view of the progressive fluorination approach. The L. lactis expression system was also used to study the role of Trp68 in the binding of riboflavin by the membrane-bound riboflavin transport protein RibU from L. lactis . Progressive fluorination of Trp68 revealed a strong electrostatic component that contributed 15-20% to the total riboflavin-RibU binding energy.


    Organizational Affiliation

    Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator, PadR-like familyA, B116Lactococcus cremorisMutation(s): 0 
Gene Names: llmg_0323
UniProt
Find proteins for A2RI36 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore A2RI36 
Go to UniProtKB:  A2RI36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2RI36
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DM1 (Subject of Investigation/LOI)
Query on DM1

Download Ideal Coordinates CCD File 
C [auth B]DAUNOMYCIN
C27 H29 N O10
STQGQHZAVUOBTE-VGBVRHCVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.495α = 90
b = 35.091β = 98.01
c = 68.074γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release