7Z06

Structure of YwlG (Q2FF14) from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Bidirectional sequestration between a bacterial hibernation factor and a glutamate metabolizing protein.

Ranava, D.Scheidler, C.M.Pfanzelt, M.Fiedler, M.Sieber, S.A.Schneider, S.Yap, M.F.

(2022) Proc Natl Acad Sci U S A 119: e2207257119-e2207257119

  • DOI: https://doi.org/10.1073/pnas.2207257119
  • Primary Citation of Related Structures:  
    7Z06

  • PubMed Abstract: 

    Bacterial hibernating 100S ribosomes (the 70S dimers) are excluded from translation and are protected from ribonucleolytic degradation, thereby promoting long-term viability and increased regrowth. No extraribosomal target of any hibernation factor has been reported. Here, we discovered a previously unrecognized binding partner (YwlG) of hibernation-promoting factor (HPF) in the human pathogen Staphylococcus aureus . YwlG is an uncharacterized virulence factor in S. aureus . We show that the HPF-YwlG interaction is direct, independent of ribosome binding, and functionally linked to cold adaptation and glucose metabolism. Consistent with the distant resemblance of YwlG to the hexameric structures of nicotinamide adenine dinucleotide (NAD)-specific glutamate dehydrogenases (GDHs), YwlG overexpression can compensate for a loss of cellular GDH activity. The reduced abundance of 100S complexes and the suppression of YwlG-dependent GDH activity provide evidence for a two-way sequestration between YwlG and HPF. These findings reveal an unexpected layer of regulation linking the biogenesis of 100S ribosomes to glutamate metabolism.


  • Organizational Affiliation

    Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0340 protein SAUSA300_2068
A, B, C, D, E
A, B, C, D, E, F
196Staphylococcus aureusMutation(s): 0 
Gene Names: SAUSA300_2068
UniProt
Find proteins for Q2FF14 (Staphylococcus aureus (strain USA300))
Explore Q2FF14 
Go to UniProtKB:  Q2FF14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FF14
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth B]
J [auth B]
K [auth B]
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
R [auth E],
S [auth E],
T [auth E],
U [auth F],
V [auth F],
W [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.741α = 90
b = 136.878β = 98.55
c = 79.19γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description