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PDBsum entry 2zdo

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2zdo
Jmol
Contents
Protein chains
108 a.a. *
Ligands
HEM ×4
Waters ×287
* Residue conservation analysis
PDB id:
2zdo
Name: Oxidoreductase
Title: Crystal structure of isdg-n7a in complex with hemin
Structure: Heme-degrading monooxygenase isdg. Chain: a, b, c, d. Synonym: iron-regulated surface determinant isdg, iron- responsive surface determinant isdg, heme oxygenase. Engineered: yes. Mutation: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Strain: n315. Gene: isdg. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.200     R-free:   0.234
Authors: W.C.Lee,M.L.Reniere,E.P.Skaar,M.E.P.Murphy
Key ref:
W.C.Lee et al. (2008). Ruffling of Metalloporphyrins Bound to IsdG and IsdI, Two Heme-degrading Enzymes in Staphylococcus aureus. J Biol Chem, 283, 30957-30963. PubMed id: 18713745 DOI: 10.1074/jbc.M709486200
Date:
27-Nov-07     Release date:   19-Aug-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q7A649  (ISDG_STAAN) -  Heme oxygenase (staphylobilin-producing) 1
Seq:
Struc:
107 a.a.
108 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 95.00% 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.M709486200 J Biol Chem 283:30957-30963 (2008)
PubMed id: 18713745  
 
 
Ruffling of Metalloporphyrins Bound to IsdG and IsdI, Two Heme-degrading Enzymes in Staphylococcus aureus.
W.C.Lee, M.L.Reniere, E.P.Skaar, M.E.Murphy.
 
  ABSTRACT  
 
IsdG and IsdI are paralogous proteins that are intracellular components of a complex heme uptake system in Staphylococcus aureus. IsdG and IsdI were shown previously to reductively degrade hemin. Crystal structures of the apoproteins show that these proteins belong to a newly identified heme degradation family distinct from canonical eukaryotic and prokaryotic heme oxygenases. Here we report the crystal structures of an inactive N7A variant of IsdG in complex with Fe(3+)-protoporphyrin IX (IsdG-hemin) and of IsdI in complex with cobalt protoporphyrin IX (IsdI-CoPPIX) to 1.8 A or better resolution. These structures show that the metalloporphyrins are buried into similar deep clefts such that the propionic acids form salt bridges to two Arg residues. His(77) (IsdG) or His(76) (IsdI), a critical residue required for activity, is coordinated to the Fe(3+) or Co(3+) atoms, respectively. The bound porphyrin rings form extensive steric interactions in the binding cleft such that the rings are highly distorted from the plane. This distortion is best described as ruffled and places the beta- and delta-meso carbons proximal to the distal oxygen-binding site. In the IsdG-hemin structure, Fe(3+) is pentacoordinate, and the distal side is occluded by the side chain of Ile(55). However, in the structure of IsdI-CoPPIX, the distal side of the CoPPIX accommodates a chloride ion in a cavity formed through a conformational change in Ile(55). The chloride ion participates in a hydrogen bond to the side chain amide of Asn(6). Together the structures suggest a reaction mechanism in which a reactive peroxide intermediate proceeds with nucleophilic oxidation at the beta- or delta-meso carbon of the hemin.
 
  Selected figure(s)  
 
Figure 3.
The structure of IsdI-CoPPIX. A, superposition of apo-IsdI (cyan) and IsdI-CoPPIX (green). The loop of IsdI-CoPPIX structure that is disordered in the apo-IsdI structure is colored red. B, active site of IsdI-CoPPIX viewed from the distal side with a F[o] - F[c] omit map contoured at 3 σ. C, active site of IsdI-CoPPIX with residues that interact with porphyrin ring depicted in stick model and labeled. In each panel, residues in the active site are depicted in the stick model and labeled. Oxygen atoms are red, nitrogen atoms are blue, and the chloride ion is a magenta sphere. CoPPIX carbons are gray, and amino acid residue carbons are colored according to the main chain of each structure.
Figure 4.
Porphyrin ring distortion analysis. NSD out-of-plane (Å) analysis (26) of the porphyrin rings from structures as follows: ChuS, E. coli HO (PDB ID 2Hq2); N-HO, Neisseria meningitidis HO (PDB ID 1J77); H-NOX, oxygen binding H-NOX domain (PDB ID 1U4H); CytC, horse heart cytochrome c (PDB ID 1HRC). Pro, wav, dom, ruf, and sad correspond to porphyrin distortions described as propeller, wave, dome, ruffle, and saddle, respectively.
 
  The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 30957-30963) copyright 2008.  
  Figures were selected by the author.  

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.  
20162612 C.Olea, M.A.Herzik, J.Kuriyan, and M.A.Marletta (2010).
Structural insights into the molecular mechanism of H-NOX activation.
  Protein Sci, 19, 881-887.
PDB codes: 3lah 3lai
20147287 J.C.Grigg, J.D.Cooper, J.Cheung, D.E.Heinrichs, and M.E.Murphy (2010).
The Staphylococcus aureus siderophore receptor HtsA undergoes localized conformational changes to enclose staphyloferrin A in an arginine-rich binding pocket.
  J Biol Chem, 285, 11162-11171.
PDB codes: 3lhs 3li2
19917297 N.Chim, A.Iniguez, T.Q.Nguyen, and C.W.Goulding (2010).
Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis.
  J Mol Biol, 395, 595-608.
PDB code: 3hx9
19398548 G.Pishchany, S.E.Dickey, and E.P.Skaar (2009).
Subcellular localization of the Staphylococcus aureus heme iron transport components IsdA and IsdB.
  Infect Immun, 77, 2624-2634.  
19564607 S.Létoffé, G.Heuck, P.Delepelaire, N.Lange, and C.Wandersman (2009).
Bacteria capture iron from heme by keeping tetrapyrrol skeleton intact.
  Proc Natl Acad Sci U S A, 106, 11719-11724.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.