7O4X

Crystal structure of the PII-like protein PotN from Lentilactobacillus hilgardii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

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This is version 1.3 of the entry. See complete history


Literature

PotN represents a novel energy-state sensing PII subfamily, occurring in firmicutes.

Iskhakova, Z.I.Zhuravleva, D.E.Heim, C.Hartmann, M.D.Laykov, A.V.Forchhammer, K.Kayumov, A.R.

(2022) FEBS J 289: 5305-5321

  • DOI: https://doi.org/10.1111/febs.16431
  • Primary Citation of Related Structures:  
    7O4X

  • PubMed Abstract: 

    PII proteins are signal processor proteins that regulate the cellular metabolism of Bacteria, Archea and plant chloroplasts typically in response to the cellular nitrogen status. Here, we report the first biochemical characterization of a novel PII-like protein PotN from Lentilactobacillus hilgardii. PotN is encoded in an operon together with the potABCD genes, encoding the ABC transporter for spermidine/putrescine. Like canonical PII proteins, the native PotN has a trimeric structure and competitively binds ATP and ADP, but it does not bind 2-oxoglutarate. Immunoprecipitation and pull-down experiments revealed that PotN is associated in vivo with the transcriptional regulator GlnR and the beta-subunit of pyruvate/2-oxoglutarate/acetoin dehydrogenase AcoB. Moreover, in vitro assays revealed that the ATPase domain of PotA also is able to interact with PotN. Interaction analyses demonstrated that PotN preferentially associates with PotA in the ADP state, whereas it binds to GlnR at elevated ATP levels. This suggests that PotN regulates the transport of polyamines and GlnR-dependent gene expression in response to the energy availability for the cell.


  • Organizational Affiliation

    Department of Genetics, Kazan Federal University, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogen regulatory protein P-II124Lentilactobacillus hilgardii ATCC 27305Mutation(s): 0 
Gene Names: HMPREF0496_1931
UniProt
Find proteins for A0A6P1EFQ2 (Lentilactobacillus hilgardii)
Explore A0A6P1EFQ2 
Go to UniProtKB:  A0A6P1EFQ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6P1EFQ2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.151α = 90
b = 80.151β = 90
c = 79.484γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-20
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2022-09-14
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description