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PDBsum entry 4fnh

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
4fnh
Jmol
Contents
Protein chains
110 a.a.
Ligands
HEM ×2
Waters ×259
PDB id:
4fnh
Name: Oxidoreductase
Title: Crystal structure of isdi-w66y in complex with heme
Structure: Heme-degrading monooxygenase isdi. Chain: a, b. Synonym: heme oxygenase, iron-regulated surface determinant iron-responsive surface determinant isdi. Engineered: yes. Mutation: yes
Source: Staphylococcus aureus subsp. Aureus. Organism_taxid: 158879. Strain: n315. Gene: isdi, sa0160. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.195     R-free:   0.230
Authors: G.N.Ukpabi,M.E.P.Murphy
Key ref: G.Ukpabi et al. (2012). Inactivation of the heme degrading enzyme IsdI by an active site substitution that diminishes heme ruffling. J Biol Chem, 287, 34179-34188. PubMed id: 22891243 DOI: 10.1074/jbc.M112.393249
Date:
19-Jun-12     Release date:   22-Aug-12    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7A827  (ISDI_STAAN) -  Heme oxygenase (staphylobilin-producing) 2
Seq:
Struc:
108 a.a.
110 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.14.99.48  - Heme oxygenase (staphylobilin-producing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
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
Protoheme
Bound ligand (Het Group name = HEM)
matches with 95.45% similarity
+ 4 × AH(2)
+ 4 × O(2)
= 5-oxo-delta-bilirubin
+ Fe(2+)
+ CO
+ 4 × A
+ 4 × H(2)O
Protoheme
+ 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  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M112.393249 J Biol Chem 287:34179-34188 (2012)
PubMed id: 22891243  
 
 
Inactivation of the heme degrading enzyme IsdI by an active site substitution that diminishes heme ruffling.
G.Ukpabi, S.J.Takayama, A.G.Mauk, M.E.Murphy.
 
  ABSTRACT  
 
IsdG and IsdI are paralogous heme degrading enzymes from the bacterium Staphylococcus aureus. Heme bound by these enzymes is extensively ruffled such that the meso-carbons at the sites of oxidation are distorted toward bound oxygen. In contrast, the canonical heme oxygenase family degrades heme that is bound with minimal distortion. Trp-66 is a conserved heme pocket residue in IsdI implicated in heme ruffling. IsdI variants with Trp-66 replaced with residues having less bulky aromatic and alkyl side chains were characterized with respect to catalytic activity, heme ruffling, and electrochemical properties. The heme degradation activity of the W66Y and W66F variants was approximately half that of the wild-type enzyme, whereas the W66L and W66A variants were inactive. A crystal structure and NMR spectroscopic analysis of the W66Y variant reveals that heme binds to this enzyme with less heme ruffling than observed for wild-type IsdI. The reduction potential of this variant (-96 ± 7 mV versus standard hydrogen electrode) is similar to that of wild-type IsdI (-89 ± 7 mV), so we attribute the diminished activity of this variant to the diminished heme ruffling observed for heme bound to this enzyme and conclude that Trp-66 is required for optimal catalytic activity.