3L9X

KefC C-terminal domain in complex with KefF and ESG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Mechanism of ligand-gated potassium efflux in bacterial pathogens.

Roosild, T.P.Castronovo, S.Healy, J.Miller, S.Pliotas, C.Rasmussen, T.Bartlett, W.Conway, S.J.Booth, I.R.

(2010) Proc Natl Acad Sci U S A 107: 19784-19789

  • DOI: 10.1073/pnas.1012716107
  • Primary Citation of Related Structures:  
    3L9W, 3L9X

  • PubMed Abstract: 
  • Gram negative pathogens are protected against toxic electrophilic compounds by glutathione-gated potassium efflux systems (Kef) that modulate cytoplasmic pH. We have elucidated the mechanism of gating through structural and functional analysis of Escherichia coli KefC ...

    Gram negative pathogens are protected against toxic electrophilic compounds by glutathione-gated potassium efflux systems (Kef) that modulate cytoplasmic pH. We have elucidated the mechanism of gating through structural and functional analysis of Escherichia coli KefC. The revealed mechanism can explain how subtle chemical differences in glutathione derivatives can produce opposite effects on channel function. Kef channels are regulated by potassium transport and NAD-binding (KTN) domains that sense both reduced glutathione, which inhibits Kef activity, and glutathione adducts that form during electrophile detoxification and activate Kef. We find that reduced glutathione stabilizes an interdomain association between two KTN folds, whereas large adducts sterically disrupt this interaction. F441 is identified as the pivotal residue discriminating between reduced glutathione and its conjugates. We demonstrate a major structural change on the binding of an activating ligand to a KTN-domain protein. Analysis of the regulatory interactions suggests strategies to disrupt pathogen potassium and pH homeostasis.


    Organizational Affiliation

    Drug Development Department, Nevada Cancer Institute, Las Vegas, NV 89135, USA. troosild@nvcancer.org



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutathione-regulated potassium-efflux system protein kefC, linker, ancillary protein kefFA, B413Escherichia coli K-12Mutation(s): 0 
Gene Names: b0047JW0046kefCtrkCb0046JW0045kefFyabF
EC: 1.6.5.2
UniProt
Find proteins for P0A754 (Escherichia coli (strain K12))
Explore P0A754 
Go to UniProtKB:  P0A754
Find proteins for P03819 (Escherichia coli (strain K12))
Explore P03819 
Go to UniProtKB:  P03819
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP03819P0A754
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
L9X
Query on L9X

Download Ideal Coordinates CCD File 
I [auth B]L-gamma-glutamyl-S-[(3R)-1-ethyl-2,5-dioxopyrrolidin-3-yl]-L-cysteinylglycine
C16 H24 N4 O8 S
QCPAUAAIPLHRLB-LPEHRKFASA-N
 Ligand Interaction
ESG
Query on ESG

Download Ideal Coordinates CCD File 
F [auth B]L-gamma-glutamyl-S-[(3S)-1-ethyl-2,5-dioxopyrrolidin-3-yl]-L-cysteinylglycine
C16 H24 N4 O8 S
QCPAUAAIPLHRLB-GUBZILKMSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.949α = 90
b = 85.941β = 90
c = 189.408γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-01
    Changes: Refinement description