6PC1

Crystal structure of Helicobacter pylori PPX/GppA (E143A) in complex with ppGpp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Currently 6PC1 does not have a validation slider image.


This is version 1.2 of the entry. See complete history


Literature

Structure and activity of PPX/GppA homologs from Escherichia coli and Helicobacter pylori.

Song, H.Dharmasena, M.N.Wang, C.Shaw, G.X.Cherry, S.Tropea, J.E.Jin, D.J.Ji, X.

(2020) FEBS J 287: 1865-1885

  • DOI: https://doi.org/10.1111/febs.15120
  • Primary Citation of Related Structures:  
    6PBZ, 6PC0, 6PC1, 6PC2, 6PC3

  • PubMed Abstract: 

    Rapid adaptation to environmental changes is crucial for bacterial survival. Almost all bacteria possess a conserved stringent response system to prompt transcriptional and metabolic responses toward stress. The adaptive process relies on alarmones, guanosine pentaphosphate (pppGpp), and tetraphosphate (ppGpp), to regulate global gene expression. The ppGpp is more potent than pppGpp in the regulatory activity, and pppGpp phosphohydrolase (GppA) plays a key role in (p)ppGpp homeostasis. Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX), which mediates the metabolism of cellular inorganic polyphosphate. Here, our phylogenetic analysis of PPX/GppA homologs in bacteria shows a wide distribution with several distinct subfamilies, and our structural and functional analysis of Escherichia coli GppA and Helicobacter pylori PPX/GppA reveals unique properties of each homolog. These results explain how each homolog possesses its distinct functionality.


  • Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanosine pentaphosphate phosphohydrolase
A, B, C, D
495Helicobacter pylori G27Mutation(s): 1 
Gene Names: HPG27_257
UniProt
Find proteins for B5ZA44 (Helicobacter pylori (strain G27))
Explore B5ZA44 
Go to UniProtKB:  B5ZA44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5ZA44
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G4P (Subject of Investigation/LOI)
Query on G4P

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
P [auth C],
U [auth D]
GUANOSINE-5',3'-TETRAPHOSPHATE
C10 H17 N5 O17 P4
BUFLLCUFNHESEH-UUOKFMHZSA-N
LMR
Query on LMR

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth B],
R [auth C],
W [auth D]
(2S)-2-hydroxybutanedioic acid
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
Q [auth C],
T [auth C],
V [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth B],
O [auth C],
S [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.507α = 90
b = 194.507β = 90
c = 136.862γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report

Currently 6PC1 does not have a validation slider image.



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary