8CIB | pdb_00008cib

Structural and functional analysis of the Pseudomonas aeruginosa PA1677 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.208 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

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

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This is version 1.0 of the entry. See complete history

Literature

Catabolite repression control protein antagonist, a novel player in Pseudomonas aeruginosa carbon catabolite repression control.

Sonnleitner, E.Bassani, F.Cianciulli Sesso, A.Brear, P.Lilic, B.Davidovski, L.Resch, A.Luisi, B.F.Moll, I.Blasi, U.

(2023) Front Microbiol 14: 1195558-1195558

  • DOI: https://doi.org/10.3389/fmicb.2023.1195558
  • Primary Citation Related Structures: 
    8CIB

  • PubMed Abstract: 

    In the opportunistic human pathogen Pseudomonas aeruginosa ( Pae ), c arbon c atabolite r epression (CCR) orchestrates the hierarchical utilization of N and C sources, and impacts virulence, antibiotic resistance and biofilm development. During CCR, the RNA chaperone Hfq and the c atabolite r epression c ontrol protein Crc form assemblies on target mRNAs that impede translation of proteins involved in uptake and catabolism of less preferred C sources. After exhaustion of the preferred C-source, translational repression of target genes is relieved by the regulatory RNA CrcZ, which binds to and acts as a decoy for Hfq. Here, we asked whether Crc action can be modulated to relieve CCR after exhaustion of a preferred carbon source. As Crc does not bind to RNA per se , we endeavored to identify an interacting protein. In vivo co-purification studies, co-immunoprecipitation and biophysical assays revealed that Crc binds to Pae strain O1 protein PA1677. Our structural studies support bioinformatics analyzes showing that PA1677 belongs to the isochorismatase-like superfamily. Ectopic expression of PA 1677 resulted in de-repression of Hfq/Crc controlled target genes, while in the absence of the protein, an extended lag phase is observed during diauxic growth on a preferred and a non-preferred carbon source. This observations indicate that PA1677 acts as an antagonist of Crc that favors synthesis of proteins required to metabolize non-preferred carbon sources. We present a working model wherein PA1677 diminishes the formation of productive Hfq/Crc repressive complexes on target mRNAs by titrating Crc. Accordingly, we propose the name CrcA ( c atabolite r epression c ontrol protein a ntagonist) for PA1677.


  • Organizational Affiliation
    • Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria.

Macromolecule Content 

  • Total Structure Weight: 135.25 kDa 
  • Atom Count: 9,892 
  • Modeled Residue Count: 1,178 
  • Deposited Residue Count: 1,254 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cysteine hydrolase
A, B, C, D, E
A, B, C, D, E, F
209Pseudomonas aeruginosaMutation(s): 0 
Gene Names: yddQ1
EC: 3.5.2.19
UniProt
Find proteins for A0A072ZIR4 (Pseudomonas aeruginosa)
Explore A0A072ZIR4 
Go to UniProtKB:  A0A072ZIR4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A072ZIR4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYS

Query on LYS



Download:Ideal Coordinates CCD File
L [auth F]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
MPD

Query on MPD



Download:Ideal Coordinates CCD File
G [auth B]
H [auth B]
J [auth D]
K [auth E]
M [auth F]
G [auth B],
H [auth B],
J [auth D],
K [auth E],
M [auth F],
N [auth F]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
I [auth D]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.208 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.284α = 90
b = 245.26β = 90
c = 126.262γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom200873/Z/16/Z
Austrian Science FundAustriaP28711-B22

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release