PDBsum entry 3lgn

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
110 a.a. *
Waters ×281
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of isdi in complex with heme
Structure: Heme-degrading monooxygenase isdi. Chain: a, b. Synonym: isdi, iron-regulated surface determinant isdi, iron-responsive surface determinant isdi, heme oxygenase. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 158879. Strain: n315. Gene: isdi. Expressed in: escherichia coli. Expression_system_taxid: 469008.
1.50Å     R-factor:   0.183     R-free:   0.214
Authors: G.N.Ukpabi,M.E.P.Murphy
Key ref: M.L.Reniere et al. (2010). The IsdG-family of haem oxygenases degrades haem to a novel chromophore. Mol Microbiol, 75, 1529-1538. PubMed id: 20180905
20-Jan-10     Release date:   09-Mar-10    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q7A827  (ISDI_STAAN) -  Heme oxygenase (staphylobilin-producing) 2
108 a.a.
110 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Heme oxygenase (staphylobilin-producing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
1. Protoheme + 4 AH2 + 4 O2 = 5-oxo-delta-bilirubin + Fe2+ + CO + 4 A + 4 H2O
2. Protoheme + 4 AH2 + 4 O2 = 15-oxo-beta-bilirubin + Fe2+ + CO + 4 A + 4 H2O
Bound ligand (Het Group name = HEM)
matches with 95.00% similarity
+ 4 × AH(2)
4 × O(2)
Bound ligand (Het Group name = OXY)
corresponds exactly
= 5-oxo-delta-bilirubin
+ Fe(2+)
+ CO
+ 4 × A
+ 4 × H(2)O
+ 4 × AH(2)
+ 4 × O(2)
= 15-oxo-beta-bilirubin
+ Fe(2+)
+ CO
+ 4 × A
+ 4 × H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     7 terms  


Mol Microbiol 75:1529-1538 (2010)
PubMed id: 20180905  
The IsdG-family of haem oxygenases degrades haem to a novel chromophore.
M.L.Reniere, G.N.Ukpabi, S.R.Harry, D.F.Stec, R.Krull, D.W.Wright, B.O.Bachmann, M.E.Murphy, E.P.Skaar.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21354424 B.Goblirsch, R.C.Kurker, B.R.Streit, C.M.Wilmot, and J.L.DuBois (2011).
Chlorite dismutases, DyPs, and EfeB: 3 microbial heme enzyme families comprise the CDE structural superfamily.
  J Mol Biol, 408, 379-398.  
21339081 J.A.Mayfield, C.A.Dehner, and J.L.DuBois (2011).
Recent advances in bacterial heme protein biochemistry.
  Curr Opin Chem Biol, 15, 260-266.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.