7JJ9

Crystal structure of Zn(II)-bound AdcA from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Trap-Door Mechanism for Zinc Acquisition by Streptococcus pneumoniae AdcA.

Luo, Z.Morey, J.R.Deplazes, E.Motygullina, A.Tan, A.Ganio, K.Neville, S.L.Eleftheriadis, N.Isselstein, M.Pederick, V.G.Paton, J.C.Cordes, T.Harmer, J.R.Kobe, B.McDevitt, C.A.

(2021) mBio 12

  • DOI: 10.1128/mBio.01958-20
  • Primary Citation of Related Structures:  
    7JJ8, 7JJ9, 7JJA, 7JJB

  • PubMed Abstract: 
  • Zinc is an essential element in all domains of life. Nonetheless, how prokaryotes achieve selective acquisition of zinc from the extracellular environment remains poorly understood. Here, we elucidate a novel mechanism for zinc-binding in AdcA, a solute-binding protein of Streptococcus pneumoniae Crystal structure analyses reveal the two-domain organization of the protein and show that only the N-terminal domain (AdcA N ) is necessary for zinc import ...

    Zinc is an essential element in all domains of life. Nonetheless, how prokaryotes achieve selective acquisition of zinc from the extracellular environment remains poorly understood. Here, we elucidate a novel mechanism for zinc-binding in AdcA, a solute-binding protein of Streptococcus pneumoniae Crystal structure analyses reveal the two-domain organization of the protein and show that only the N-terminal domain (AdcA N ) is necessary for zinc import. Zinc binding induces only minor changes in the global protein conformation of AdcA and stabilizes a highly mobile loop within the AdcA N domain. This loop region, which is conserved in zinc-specific solute-binding proteins, facilitates closure of the AdcA N binding site and is crucial for zinc acquisition. Collectively, these findings elucidate the structural and functional basis of selective zinc uptake in prokaryotes. IMPORTANCE Zinc is an essential nutrient for the virulence of bacterial pathogens such as Streptococcus pneumoniae Many Gram-positive bacteria use a two-domain lipoprotein for zinc acquisition, but how this class of metal-recruiting proteins acquire zinc and interact with the uptake machinery has remained poorly defined. We report the first structure of a two-domain lipoprotein, AdcA from S. pneumoniae , and use computational, spectroscopic, and microbiological approaches to provide new insights into the functional basis of zinc recruitment. Our findings reveal that AdcA employs a novel mechanism for zinc binding that we have termed the "trap-door" mechanism, and we show how the static metal-binding site of the protein, which confers its selectivity for zinc ions, is combined with a dynamic surface element to facilitate zinc recruitment and import into the bacterium. Together, these findings expand our understanding of how bacteria acquire zinc from the environment and provide a foundation for inhibiting this process, through antimicrobial targeting of the dynamic structural elements to block bacterial zinc scavenging.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc-binding lipoprotein AdcAA475Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: adcAspr1975
UniProt
Find proteins for Q8CWN2 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8CWN2 
Go to UniProtKB:  Q8CWN2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8CWN2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.109α = 90
b = 44.362β = 106.825
c = 92.627γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1071659
National Health and Medical Research Council (NHMRC, Australia)Australia1080784
National Health and Medical Research Council (NHMRC, Australia)Australia1122582
Australian Research Council (ARC)AustraliaDP170102102

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references