3L9X | pdb_00003l9x

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 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1073/pnas.1012716107
  • Primary Citation 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. 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

Macromolecule Content 

  • Total Structure Weight: 95.22 kDa 
  • Atom Count: 5,774 
  • Modeled Residue Count: 672 
  • Deposited Residue Count: 826 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione-regulated potassium-efflux system protein kefC, linker, ancillary protein kefF
A, B
413Escherichia coli K-12Mutation(s): 0 
Gene Names: b0047JW0046kefCtrkCb0046JW0045kefFyabF
EC: 1.6.5.2
UniProt
Find proteins for P03819 (Escherichia coli (strain K12))
Explore P03819 
Go to UniProtKB:  P03819
Find proteins for P0A754 (Escherichia coli (strain K12))
Explore P0A754 
Go to UniProtKB:  P0A754
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0A754P03819
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / 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
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
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
SO4

Query on SO4



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

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.236 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
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

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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
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description