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PDBsum entry 1e93

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Oxidoreductase PDB id
1e93
Jmol
Contents
Protein chain
476 a.a. *
Ligands
HEM
ACT
SO4
Waters ×614
* Residue conservation analysis
PDB id:
1e93
Name: Oxidoreductase
Title: High resolution structure and biochemical properties of a recombinant catalase depleted in iron
Structure: Catalase. Chain: a. Engineered: yes. Other_details: methionine sulfone in position 53 tyrosine 337 lack the hydroxyl hydrogen
Source: Proteus mirabilis. Organism_taxid: 584. Gene: kata. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
2.00Å     R-factor:   0.199     R-free:   0.215
Authors: P.Andreoletti,G.Sainz,M.Jaquinod,J.Gagnon,H.M.Jouve
Key ref:
P.Andreoletti et al. (2003). High-resolution structure and biochemical properties of a recombinant Proteus mirabilis catalase depleted in iron. Proteins, 50, 261-271. PubMed id: 12486720 DOI: 10.1002/prot.10283
Date:
05-Oct-00     Release date:   13-Oct-00    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P42321  (CATA_PROMI) -  Catalase
Seq:
Struc:
484 a.a.
476 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.6  - Catalase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 H2O2 = O2 + 2 H2O
2 × H(2)O(2)
= O(2)
+ 2 × H(2)O
      Cofactor: Heme; Mn(2+)
Heme
Bound ligand (Het Group name = HEM) matches with 95.00% similarity
Mn(2+)
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     5 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.10283 Proteins 50:261-271 (2003)
PubMed id: 12486720  
 
 
High-resolution structure and biochemical properties of a recombinant Proteus mirabilis catalase depleted in iron.
P.Andreoletti, G.Sainz, M.Jaquinod, J.Gagnon, H.M.Jouve.
 
  ABSTRACT  
 
Heme catalases are homotetrameric enzymes with a highly conserved complex quaternary structure, and their functional role is still not well understood. Proteus mirabilis catalase (PMC), a heme enzyme belonging to the family of NADPH-binding catalases, was efficiently overexpressed in E. coli. The recombinant catalase (rec PMC) was deficient in heme with one-third heme and two-thirds protoporphyrin IX as determined by mass spectrometry and chemical methods. This ratio was influenced by the expression conditions, but the enzyme-specific activity calculated relative to the heme content remained unchanged. The crystal structure of rec PMC was solved to a resolution of 2.0 A, the highest resolution obtained to date with PMC. The overall structure was quite similar to that of wild-type PMC, and it is surprising that the absence of iron had no effect on the structure of the active site. Met 53 close to the essential His 54 was found less oxidized in rec PMC than in the wild-type enzyme. An acetate anion was modeled in an anionic pocket, away from the heme group but important for the enzymatic reaction. An alternate conformation observed for Arg 99 could play a role in the formation of the H-bond network connecting two symmetrical subunits of the tetramer.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. View of the 2Fo-Fc and the Fo-Fc electron density maps around the heme. The 2Fo-Fc electron density map around the heme was contoured at 1 and shown in light gray. The Fo-Fc difference map contoured at 3 shows a negative density (in dark gray) around the iron atom, suggesting an excess of electrons in the model. The resolution is 2 Å.
Figure 7.
Figure 7. Ball-and-stick representation of the heme and the acetate anion. The acetate anion was modeled in the anion-binding site, located at about 16 Å from iron on the proximal side of the heme.[33] It formed H-bonds (dashed lines) with surrounding amino acid residues (Arg 342 and His 349 of the same subunit and His 42 of the Q-related subunit) and with water molecules (W 137 and W 458) designed as black balls.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2003, 50, 261-271) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20553500 M.Brugna, L.Tasse, and L.Hederstedt (2010).
In vivo production of catalase containing haem analogues.
  FEBS J, 277, 2663-2672.  
17237942 O.Horner, J.M.Mouesca, P.L.Solari, M.Orio, J.L.Oddou, P.Bonville, and H.M.Jouve (2007).
Spectroscopic description of an unusual protonated ferryl species in the catalase from Proteus mirabilis and density functional theory calculations on related models. Consequences for the ferryl protonation state in catalase, peroxidase and chloroperoxidase.
  J Biol Inorg Chem, 12, 509-525.  
16609813 M.S.Lorentzen, E.Moe, H.M.Jouve, and N.P.Willassen (2006).
Cold adapted features of Vibrio salmonicida catalase: characterisation and comparison to the mesophilic counterpart from Proteus mirabilis.
  Extremophiles, 10, 427-440.  
14573945 E.Girard, M.Stelter, J.Vicat, and R.Kahn (2003).
A new class of lanthanide complexes to obtain high-phasing-power heavy-atom derivatives for macromolecular crystallography.
  Acta Crystallogr D Biol Crystallogr, 59, 1914-1922.  
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