4QRH

Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


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Literature

Molecular Mechanism and Evolution of Guanylate Kinase Regulation by (p)ppGpp.

Liu, K.Myers, A.R.Pisithkul, T.Claas, K.R.Satyshur, K.A.Amador-Noguez, D.Keck, J.L.Wang, J.D.

(2015) Mol Cell 57: 735-749

  • DOI: https://doi.org/10.1016/j.molcel.2014.12.037
  • Primary Citation of Related Structures:  
    4QRH

  • PubMed Abstract: 

    The nucleotide (p)ppGpp mediates bacterial stress responses, but its targets and underlying mechanisms of action vary among bacterial species and remain incompletely understood. Here, we characterize the molecular interaction between (p)ppGpp and guanylate kinase (GMK), revealing the importance of this interaction in adaptation to starvation. Combining structural and kinetic analyses, we show that (p)ppGpp binds the GMK active site and competitively inhibits the enzyme. The (p)ppGpp-GMK interaction prevents the conversion of GMP to GDP, resulting in GMP accumulation upon amino acid downshift. Abolishing this interaction leads to excess (p)ppGpp and defective adaptation to amino acid starvation. A survey of GMKs from phylogenetically diverse bacteria shows that the (p)ppGpp-GMK interaction is conserved in members of Firmicutes, Actinobacteria, and Deinococcus-Thermus, but not in Proteobacteria, where (p)ppGpp regulates RNA polymerase (RNAP). We propose that GMK is an ancestral (p)ppGpp target and RNAP evolved more recently as a direct target in Proteobacteria.


  • Organizational Affiliation

    Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: wang@bact.wisc.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanylate kinase
A, B, C, D
210Staphylococcus aureus USA300-ISMMS1Mutation(s): 0 
Gene Names: gmkAZ30_05805
EC: 2.7.4.8
UniProt
Find proteins for A0A0J9X1Z9 (Staphylococcus aureus USA300-ISMMS1)
Explore A0A0J9X1Z9 
Go to UniProtKB:  A0A0J9X1Z9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J9X1Z9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0O2
Query on 0O2

Download Ideal Coordinates CCD File 
H [auth B],
L [auth C],
R [auth D]
guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)
C10 H18 N5 O20 P5
KCPMACXZAITQAX-UUOKFMHZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
K [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
O [auth D],
P [auth D],
Q [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
G [auth B],
J [auth C],
N [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth B],
I [auth C],
M [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
0O2 Binding MOAD:  4QRH Ki: 7000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.486α = 90
b = 93.961β = 111.09
c = 85.259γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description