5YHE | pdb_00005yhe

The crystal structure of Staphylococcus aureus CntA in complex with staphylopine and cobalt


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.234 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Mechanistic insights into staphylopine-mediated metal acquisition

Song, L.Zhang, Y.Chen, W.Gu, T.Zhang, S.Y.Ji, Q.

(2018) Proc Natl Acad Sci U S A 115: 3942-3947

  • DOI: https://doi.org/10.1073/pnas.1718382115
  • Primary Citation Related Structures: 
    5YH5, 5YH8, 5YHE, 5YHG

  • PubMed Abstract: 

    Metal acquisition is vital to pathogens for successful infection within hosts. Staphylopine (StP), a broad-spectrum metallophore biosynthesized by the major human pathogen, Staphylococcus aureus , plays a central role in transition-metal acquisition and bacterial virulence. The StP-like biosynthesis loci are present in various pathogens, and the proteins responsible for StP/metal transportation have been determined. However, the molecular mechanisms of how StP/metal complexes are recognized and transported remain unknown. We report multiple structures of the extracytoplasmic solute-binding protein CntA from the StP/metal transportation system in apo form and in complex with StP and three different metals. We elucidated a sophisticated metal-bound StP recognition mechanism and determined that StP/metal binding triggers a notable interdomain conformational change in CntA. Furthermore, CRISPR/Cas9-mediated single-base substitution mutations and biochemical analysis highlight the importance of StP/metal recognition for StP/metal acquisition. These discoveries provide critical insights into the study of novel metal-acquisition mechanisms in microbes.


  • Organizational Affiliation
    • School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 116.31 kDa 
  • Atom Count: 8,525 
  • Modeled Residue Count: 1,013 
  • Deposited Residue Count: 1,016 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nickel ABC transporter substrate-binding protein
A, B
508Staphylococcus aureusMutation(s): 0 
Gene Names: opp-1AAYM28_13740AYM37_13740ERS072738_00487ERS074020_00717HMPREF3211_02361
UniProt
Find proteins for Q2FVE7 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FVE7 
Go to UniProtKB:  Q2FVE7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FVE7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8UX
(Subject of Investigation/LOI)

Query on 8UX



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B]
(2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid
C13 H20 N4 O6
WLNNYKMTYVPSDL-UJNFCWOMSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
H [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CO
(Subject of Investigation/LOI)

Query on CO



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.234 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.605α = 90.68
b = 76.659β = 91.25
c = 85.673γ = 104.57
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references