2R79

Crystal Structure of a Periplasmic Heme Binding Protein from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

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This is version 1.2 of the entry. See complete history


Literature

Holo- and apo-bound structures of bacterial periplasmic heme-binding proteins.

Ho, W.W.Li, H.Eakanunkul, S.Tong, Y.Wilks, A.Guo, M.Poulos, T.L.

(2007) J Biol Chem 282: 35796-35802

  • DOI: https://doi.org/10.1074/jbc.M706761200
  • Primary Citation of Related Structures:  
    2R79, 2R7A, 2RG7

  • PubMed Abstract: 

    An essential component of heme transport in Gram-negative bacterial pathogens is the periplasmic protein that shuttles heme between outer and inner membranes. We have solved the first crystal structures of two such proteins, ShuT from Shigella dysenteriae and PhuT from Pseudomonas aeruginosa. Both share a common architecture typical of Class III periplasmic binding proteins. The heme binds in a narrow cleft between the N- and C-terminal binding domains and is coordinated by a Tyr residue. A comparison of the heme-free (apo) and -bound (holo) structures indicates little change in structure other than minor alterations in the heme pocket and movement of the Tyr heme ligand from an "in" position where it can coordinate the heme iron to an "out" orientation where it points away from the heme pocket. The detailed architecture of the heme pocket is quite different in ShuT and PhuT. Although Arg(228) in PhuT H-bonds with a heme propionate, in ShuT a peptide loop partially takes up the space occupied by Arg(228), and there is no Lys or Arg H-bonding with the heme propionates. A comparison of PhuT/ShuT with the vitamin B(12)-binding protein BtuF and the hydroxamic-type siderophore-binding protein FhuD, the only two other structurally characterized Class III periplasmic binding proteins, demonstrates that PhuT/ShuT more closely resembles BtuF, which reflects the closer similarity in ligands, heme and B(12), compared with ligands for FhuD, a peptide siderophore.


  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic binding protein283Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for O68879 (Pseudomonas aeruginosa)
Explore O68879 
Go to UniProtKB:  O68879
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68879
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.913α = 90
b = 132.913β = 90
c = 72.93γ = 120
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations