7T50

Crystal structure of the molybdate-binding periplasmic protein ModA from the bacteria Pseudomonsa aeruginosa in chromate-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Impact of Chromate on Pseudomonas aeruginosa Molybdenum Homeostasis.

Maunders, E.A.Ngu, D.H.Y.Ganio, K.Hossain, S.I.Lim, B.Y.J.Leeming, M.G.Luo, Z.Tan, A.Deplazes, E.Kobe, B.McDevitt, C.A.

(2022) Front Microbiol 13: 903146-903146

  • DOI: https://doi.org/10.3389/fmicb.2022.903146
  • Primary Citation of Related Structures:  
    7T4Z, 7T50, 7T51, 7T5A

  • PubMed Abstract: 

    Acquisition of the trace-element molybdenum via the high-affinity ATP-binding cassette permease ModABC is essential for Pseudomonas aeruginosa respiration in anaerobic and microaerophilic environments. This study determined the X-ray crystal structures of the molybdenum-recruiting solute-binding protein ModA from P. aeruginosa PAO1 in the metal-free state and bound to the group 6 metal oxyanions molybdate, tungstate, and chromate. Pseudomonas aeruginosa PAO1 ModA has a non-contiguous dual-hinged bilobal structure with a single metal-binding site positioned between the two domains. Metal binding results in a 22° relative rotation of the two lobes with the oxyanions coordinated by four residues, that contribute six hydrogen bonds, distinct from ModA orthologues that feature an additional oxyanion-binding residue. Analysis of 485 Pseudomonas ModA sequences revealed conservation of the metal-binding residues and β-sheet structural elements, highlighting their contribution to protein structure and function. Despite the capacity of ModA to bind chromate, deletion of modA did not affect P. aeruginosa PAO1 sensitivity to chromate toxicity nor impact cellular accumulation of chromate. Exposure to sub-inhibitory concentrations of chromate broadly perturbed P. aeruginosa metal homeostasis and, unexpectedly, was associated with an increase in ModA-mediated molybdenum uptake. Elemental analyses of the proteome from anaerobically grown P. aeruginosa revealed that, despite the increase in cellular molybdenum upon chromate exposure, distribution of the metal within the proteome was substantially perturbed. This suggested that molybdoprotein cofactor acquisition may be disrupted, consistent with the potent toxicity of chromate under anaerobic conditions. Collectively, these data reveal a complex relationship between chromate toxicity, molybdenum homeostasis and anaerobic respiration.


  • Organizational Affiliation

    Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Molybdate-binding periplasmic protein ModA
A, B
231Pseudomonas aeruginosa PA1Mutation(s): 0 
Gene Names: modA
UniProt
Find proteins for Q9I2N2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I2N2 
Go to UniProtKB:  Q9I2N2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I2N2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CQ4 (Subject of Investigation/LOI)
Query on CQ4

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
Chromate
Cr O4
ZCDOYSPFYFSLEW-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NH4
Query on NH4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth A],
K [auth B]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.627α = 90
b = 41.223β = 92.758
c = 111.366γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaLE170100200
National Health and Medical Research Council (NHMRC, Australia)Australia1071659
National Health and Medical Research Council (NHMRC, Australia)Australia1122582
National Health and Medical Research Council (NHMRC, Australia)Australia1180826
Australian Research Council (ARC)AustraliaDP170102102
Australian Research Council (ARC)AustraliaFL180100109
Australian Research Council (ARC)AustraliaFT170100006

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description