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 8WCT | pdb_00008wct

The crystal structure of the CHASE4 domain of iron-sensetive membrane protein (IsmP,Uniprot ID:Q9I243)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.263 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8WCT

This is version 1.1 of the entry. See complete history. 

Literature

A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa.

Zhan, X., Zhang, K., Wang, C., Fan, Q., Tang, X., Zhang, X., Wang, K., Fu, Y., Liang, H.

(2024) Nat Commun 15: 1860-1860

  • DOI: https://doi.org/10.1038/s41467-024-46149-3
  • Primary Citation Related Structures: 
    8WCN, 8WCT

  • PubMed Abstract: 

    Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a bacterial second messenger that modulates various processes including biofilm formation, motility, and host-microbe symbiosis. Numerous studies have conducted comprehensive analysis of c-di-GMP. However, the mechanisms by which certain environmental signals such as iron control intracellular c-di-GMP levels are unclear. Here, we show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein, IsmP, and a diguanylate cyclase, ImcA. Binding of iron to the CHASE4 domain of IsmP inhibits the IsmP-ImcA interaction, which leads to increased c-di-GMP synthesis by ImcA, thus promoting biofilm formation and reducing bacterial motility. Structural characterization of the apo-CHASE4 domain and its binding to iron allows us to pinpoint residues defining its specificity. In addition, the cryo-electron microscopy structure of ImcA in complex with a c-di-GMP analog (GMPCPP) suggests a unique conformation in which the compound binds to the catalytic pockets and to the membrane-proximal side located at the cytoplasm. Thus, our results indicate that a CHASE4 domain directly senses iron and modulates the crosstalk between c-di-GMP metabolic enzymes.


  • Organizational Affiliation: 
    • College of Life Sciences, Northwest University, Xi'an, ShaanXi, China.

Macromolecule Content 

  • Total Structure Weight: 54.34 kDa 
  • Atom Count: 3,670 
  • Modeled Residue Count: 428 
  • Deposited Residue Count: 500 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional diguanylate cyclase/phosphodiesterase
A, B
250Pseudomonas aeruginosaMutation(s): 0 
Gene Names: PA2072
UniProt
Find proteins for Q9I243 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I243 
Go to UniProtKB:  Q9I243
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I243
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.263 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.431α = 90
b = 75.205β = 90
c = 104.08γ = 90
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-02-14 
  • Deposition Author(s): Wang, C.C.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references