5EC6

The apo crystal structure of haemoglobin receptor HpuA from Kingella denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Structural analysis of haemoglobin binding by HpuA from the Neisseriaceae family.

Wong, C.T.Xu, Y.Gupta, A.Garnett, J.A.Matthews, S.J.Hare, S.A.

(2015) Nat Commun 6: 10172-10172

  • DOI: https://doi.org/10.1038/ncomms10172
  • Primary Citation of Related Structures:  
    5EC6, 5EE2, 5EE4

  • PubMed Abstract: 

    The Neisseriaceae family of bacteria causes a range of diseases including meningitis, septicaemia, gonorrhoea and endocarditis, and extracts haem from haemoglobin as an important iron source within the iron-limited environment of its human host. Herein we report crystal structures of apo- and haemoglobin-bound HpuA, an essential component of this haem import system. The interface involves long loops on the bacterial receptor that present hydrophobic side chains for packing against the surface of haemoglobin. Interestingly, our structural and biochemical analyses of Kingella denitrificans and Neisseria gonorrhoeae HpuA mutants, although validating the interactions observed in the crystal structure, show how Neisseriaceae have the fascinating ability to diversify functional sequences and yet retain the haemoglobin binding function. Our results present the first description of HpuA's role in direct binding of haemoglobin.


  • Organizational Affiliation

    Department of Life Sciences, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin-haptoglobin-utilization protein322Kingella denitrificans ATCC 33394Mutation(s): 0 
Gene Names: HMPREF9098_0447
UniProt
Find proteins for F0EX68 (Kingella denitrificans ATCC 33394)
Explore F0EX68 
Go to UniProtKB:  F0EX68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF0EX68
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.47α = 90
b = 102.47β = 90
c = 77.21γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG1100332

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2015-12-30
    Changes: Database references
  • Version 2.0: 2017-09-13
    Changes: Atomic model, Author supporting evidence
  • Version 2.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 2.2: 2019-10-23
    Changes: Data collection, Database references
  • Version 3.0: 2023-03-15
    Changes: Advisory, Database references, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary