3LGM

Crystal structure of reduced IsdI in complex with heme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The IsdG-family of haem oxygenases degrades haem to a novel chromophore

Reniere, M.L.Ukpabi, G.N.Harry, S.R.Stec, D.F.Krull, R.Wright, D.W.Bachmann, B.O.Murphy, M.E.P.Skaar, E.P.

(2010) Mol Microbiol 75: 1529-1538

  • DOI: https://doi.org/10.1111/j.1365-2958.2010.07076.x
  • Primary Citation of Related Structures:  
    3LGM, 3LGN

  • PubMed Abstract: 

    Enzymatic haem catabolism by haem oxygenases is conserved from bacteria to humans and proceeds through a common mechanism leading to the formation of iron, carbon monoxide and biliverdin. The first members of a novel class of haem oxygenases were recently identified in Staphylococcus aureus (IsdG and IsdI) and were termed the IsdG-family of haem oxygenases. Enzymes of the IsdG-family form tertiary structures distinct from those of the canonical haem oxygenase family, suggesting that IsdG-family members degrade haem via a unique reaction mechanism. Herein we report that the IsdG-family of haem oxygenases degrade haem to the oxo-bilirubin chromophore staphylobilin. We also present the crystal structure of haem-bound IsdI in which haem ruffling and constrained binding of oxygen is consistent with cleavage of the porphyrin ring at the beta- or delta-meso carbons. Combined, these data establish that the IsdG-family of haem oxygenases degrades haem to a novel chromophore distinct from biliverdin.


  • Organizational Affiliation

    Department of Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heme-degrading monooxygenase isdI
A, B
110Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: IsdI
EC: 1.14.99.3
UniProt
Find proteins for Q7A827 (Staphylococcus aureus (strain N315))
Explore Q7A827 
Go to UniProtKB:  Q7A827
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7A827
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.04α = 90
b = 68.03β = 90
c = 70.75γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description