5YH5

The crystal structure of Staphylococcus aureus CntA in apo form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 

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:  
    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 ...

    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; quanjiangji@shanghaitech.edu.cn.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nickel ABC transporter substrate-binding proteinA507Staphylococcus aureusMutation(s): 0 
Gene Names: opp-1A, AYM28_13740, AYM37_13740, ERS072738_00487, ERS074020_00717, HMPREF3211_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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG
Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.395α = 90
b = 149.395β = 90
c = 53.635γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

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

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, Derived calculations, Structure summary
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references, Derived calculations, Structure summary