5B57

Inward-facing conformation of ABC heme importer BhuUV from Burkholderia cenocepacia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of bacterial haem importer complex in the inward-facing conformation

Naoe, Y.Nakamura, N.Doi, A.Sawabe, M.Nakamura, H.Shiro, Y.Sugimoto, H.

(2016) Nat Commun 7: 13411-13411

  • DOI: https://doi.org/10.1038/ncomms13411
  • Primary Citation of Related Structures:  
    5B57, 5B58

  • PubMed Abstract: 

    Pathogenic bacteria remove iron from the haem of host tissues and use it as a catalytic center of many enzymes. Haem uptake by pathogenic bacteria is facilitated by the membrane-integrated haem importer, which belongs to the type II ATP-binding cassette (ABC) transporter. Here we present crystal structures of Burkholderia cenocepacia haem importer BhuUV complexed with the periplasmic haem-binding protein BhuT and in the absence of BhuT. The transmembrane helices of these structures show an inward-facing conformation, in which the cytoplasmic gate of the haem translocation pathway is completely open. Since this conformation is found in both the haem- and nucleotide-free form, the structure of BhuUV-T provides the post-translocation state and the missing piece in the transport cycle of the type II importer. Structural comparison with the outward-facing conformation reported for the haem importer ortholog HmuUV from Yersenia pestis gives mechanistic insights into conformational transitions and haem secretion during the haem transport cycle.


  • Organizational Affiliation

    Biometal Science Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative hemin ABC transport system, membrane protein
A, B
385Burkholderia cenocepacia J2315Mutation(s): 0 
Gene Names: hmuUBCAM2629
Membrane Entity: Yes 
UniProt
Find proteins for B4EKB4 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Explore B4EKB4 
Go to UniProtKB:  B4EKB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4EKB4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemin import ATP-binding protein HmuV
C, D
273Burkholderia cenocepacia J2315Mutation(s): 0 
Gene Names: hmuVBCAM2630
EC: 3.6.3
Membrane Entity: Yes 
UniProt
Find proteins for B4EKB5 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Explore B4EKB5 
Go to UniProtKB:  B4EKB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4EKB5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.824α = 90
b = 118.283β = 90
c = 142.747γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan23121531
JSPSJapan24687015
JSPSJapan25121739
JSPSJapan15H01655

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-11-23
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references
  • Version 1.4: 2024-04-03
    Changes: Refinement description