4G1U

X-ray structure of the bacterial heme transporter HmuUV from Yersinia pestis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 

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Literature

X-ray structure of the Yersinia pestis heme transporter HmuUV.

Woo, J.-S., Zeltina, A., Goetz, B.A., Locher, K.P.

(2012) Nat Struct Mol Biol 19: 1310-1315

  • DOI: 10.1038/nsmb.2417
  • Primary Citation of Related Structures:  
    4G1U

  • PubMed Abstract: 

    • HmuUV is a bacterial ATP-binding cassette (ABC) transporter that catalyzes heme uptake into the cytoplasm of the gram-negative pathogen Yersinia pestis. We report the crystal structure of HmuUV at 3.0 Å resolution in a nucleotide-free state, which features a heme translocation pathway in an outward-facing conformation, poised to accept a heme from the cognate periplasmic binding protein HmuT ...

    HmuUV is a bacterial ATP-binding cassette (ABC) transporter that catalyzes heme uptake into the cytoplasm of the gram-negative pathogen Yersinia pestis. We report the crystal structure of HmuUV at 3.0 Å resolution in a nucleotide-free state, which features a heme translocation pathway in an outward-facing conformation, poised to accept a heme from the cognate periplasmic binding protein HmuT. A new assay allowed us to determine in vitro rates of HmuUV-catalyzed heme transport into proteoliposomes and to establish the role of conserved residues in the translocation pathway of HmuUV and at the interface with HmuT. Differences in architecture relative to the related vitamin B(12) transporter BtuCD suggest an adaptation of HmuUV for its smaller substrate. Our study also suggests that type II ABC importers, which include bacterial iron-siderophore, heme and cobalamin transporters, have a coupling mechanism distinct from that of other ABC transporters.

    Organizational Affiliation: 

    Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, CH-8093 Zürich, Switzerland.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hemin transport system permease protein hmuUA, B357Yersinia pestisMutation(s): 0 
Gene Names: hmuU, YPO0280, y0540, YP_0435
Membrane Entity: Yes 
UniProt
Find proteins for Q56992 (Yersinia pestis)
Explore Q56992 
Go to UniProtKB:  Q56992
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56992
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hemin import ATP-binding protein HmuVC, D266Yersinia pestisMutation(s): 0 
Gene Names: hmuV, YPO0279, y0539, YP_0434
EC: 3.6.3 (PDB Primary Data), 7.6.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q56993 (Yersinia pestis)
Explore Q56993 
Go to UniProtKB:  Q56993
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56993
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
E [auth C],
F [auth D]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.265 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.87α = 90
b = 101.23β = 91.3
c = 105.21γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
SHELXSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-19
    Type: Initial release