5YH8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1073/pnas.1718382115
  • Primary Citation of Related Structures:  

  • 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, <i>Staphylococcus aureus </i>, plays a central role in transition-metal acqu ...

    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 Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 200240 Shanghai, China.,School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, China.,School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai, China; quanjiangji@shanghaitech.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nickel ABC transporter substrate-binding protein
A
510Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: cntA (opp-1A, opp1A)
Find proteins for Q2FVE7 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FVE7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
8UX
Query on 8UX

Download SDF File 
Download CCD File 
A
(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
staphylopine
C13 H20 N4 O6
WLNNYKMTYVPSDL-UJNFCWOMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.155 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.782α = 90.00
b = 85.474β = 90.00
c = 86.315γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
REFMACrefinement
PHASERphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-27 
  • Released Date: 2018-03-28 
  • Deposition Author(s): Ji, Q., Song, L.

Revision History 

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