5KAW

The structure of SAV2435 bound to TETRAPHENYLPHOSPHONIUM and RHODAMINE 6G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Solution Binding and Structural Analyses Reveal Potential Multidrug Resistance Functions for SAV2435 and CTR107 and Other GyrI-like Proteins.

Moreno, A.Froehlig, J.R.Bachas, S.Gunio, D.Alexander, T.Vanya, A.Wade, H.

(2016) Biochemistry 55: 4850-4863

  • DOI: 10.1021/acs.biochem.6b00651
  • Primary Citation of Related Structures:  
    5KAT, 5KAU, 5KAV, 5KAW, 5KAX, 5KCB

  • PubMed Abstract: 
  • Multidrug resistance (MDR) refers to the acquired ability of cells to tolerate a broad range of toxic compounds. One mechanism cells employ is to increase the level of expression of efflux pumps for the expulsion of xenobiotics. A key feature uniting efflux-related mechanisms is multidrug (MD) recognition, either by efflux pumps themselves or by their transcriptional regulators ...

    Multidrug resistance (MDR) refers to the acquired ability of cells to tolerate a broad range of toxic compounds. One mechanism cells employ is to increase the level of expression of efflux pumps for the expulsion of xenobiotics. A key feature uniting efflux-related mechanisms is multidrug (MD) recognition, either by efflux pumps themselves or by their transcriptional regulators. However, models describing MD binding by MDR effectors are incomplete, underscoring the importance of studies focused on the recognition elements and key motifs that dictate polyspecific binding. One such motif is the GyrI-like domain, which is found in several MDR proteins and is postulated to have been adapted for small-molecule binding and signaling. Here we report the solution binding properties and crystal structures of two proteins containing GyrI-like domains, SAV2435 and CTR107, bound to various ligands. Furthermore, we provide a comparison with deposited crystal structures of GyrI-like proteins, revealing key features of GyrI-like domains that not only support polyspecific binding but also are conserved among GyrI-like domains. Together, our studies suggest that GyrI-like domains perform evolutionarily conserved functions connected to multidrug binding and highlight the utility of these types of studies for elucidating mechanisms of MDR.


    Organizational Affiliation

    Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SA2223 proteinA165Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: SA2223
UniProt
Find proteins for A0A0H3JRN6 (Staphylococcus aureus (strain N315))
Explore A0A0H3JRN6 
Go to UniProtKB:  A0A0H3JRN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JRN6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RHQ
Query on RHQ

Download Ideal Coordinates CCD File 
B [auth A]RHODAMINE 6G
C28 H31 N2 O3
IWWWBRIIGAXLCJ-KRUMMXJUSA-O
 Ligand Interaction
P4P
Query on P4P

Download Ideal Coordinates CCD File 
C [auth A]TETRAPHENYLPHOSPHONIUM
C24 H20 P
USFPINLPPFWTJW-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.724α = 90
b = 73.724β = 90
c = 65.891γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-06-02 
  • Released Date: 2016-08-24 
  • Deposition Author(s): Moreno, A., Wade, H.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-0953430
Arnold and Mabel Beckman Young Investigator AwardUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence, Database references, Derived calculations