8UUB

Structure of hypothiocyanous acid reductase (Har) from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Hypothiocyanous acid reductase is critical for host colonization and infection by Streptococcus pneumoniae.

Shearer, H.L.Currie, M.J.Agnew, H.N.Trappetti, C.Stull, F.Pace, P.E.Paton, J.C.Dobson, R.C.J.Dickerhof, N.

(2024) J Biol Chem : 107282-107282

  • DOI: https://doi.org/10.1016/j.jbc.2024.107282
  • Primary Citation of Related Structures:  
    8UUB

  • PubMed Abstract: 

    The major human pathogen Streptococcus pneumoniae encounters the immune-derived oxidant hypothiocyanous acid (HOSCN) at sites of colonization and infection. We recently identified the pneumococcal hypothiocyanous acid reductase (Har), a member of the flavoprotein disulfide reductase enzyme family, and showed that it contributes to the HOSCN tolerance of S. pneumoniae in vitro. Here, we demonstrate in mouse models of pneumococcal infection that Har is critical for colonization and invasion. In a colonization model, bacterial load was attenuated dramatically in the nasopharynx when har was deleted in S. pneumoniae. The Δhar strain was also less virulent compared to wild type in an invasion model as reflected by a significant reduction in bacteria in the lungs and no dissemination to the blood and brain. Kinetic measurements with recombinant Har demonstrated that this enzyme reduced HOSCN with near diffusion limited catalytic efficiency, using either NADH (k cat /K M = 1.2 x 10 8 M -1 s -1 ) or NADPH (k cat /K M = 2.5 x 10 7 M -1 s -1 ) as electron donors. We determined the X-ray crystal structure of Har in complex with the FAD cofactor to 1.50 Å resolution, highlighting the active site architecture characteristic for this class of enzymes. Collectively, our results demonstrate that pneumococcal Har is a highly efficient HOSCN reductase, enabling survival against oxidative host immune defenses. In addition, we provide structural insights that may aid the design of Har inhibitors.


  • Organizational Affiliation

    Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand; Biomolecular Interaction Centre, MacDiarmid Institute for Advanced Materials and Nanotechnology and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxidoreductase, pyridine nucleotide-disulfide, class I442Streptococcus pneumoniae D39Mutation(s): 0 
Gene Names: SPD_1415
UniProt
Find proteins for A0A0H2ZMK9 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466))
Explore A0A0H2ZMK9 
Go to UniProtKB:  A0A0H2ZMK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZMK9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MLI
Query on MLI

Download Ideal Coordinates CCD File 
C [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.259α = 90
b = 122.259β = 90
c = 92.439γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MrBUMPphasing
Cootmodel building
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Health Research Council (HRC)New Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Database references