PDBsum entry 1si8

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Oxidoreductase PDB id
Protein chains
474 a.a. *
SO4 ×8
HEM ×4
_CL ×2
Waters ×1195
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Crystal structure of e. Faecalis catalase
Structure: Catalase. Chain: a, b, c, d. Synonym: catalase/peroxidase. Engineered: yes
Source: Enterococcus faecalis. Organism_taxid: 226185. Strain: v583. Gene: kata. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
Biol. unit: Tetramer (from PQS)
2.30Å     R-factor:   0.202     R-free:   0.218
Authors: K.O.Hakansson,M.Brugna,L.Tasse
Key ref:
K.O.Håkansson et al. (2004). The three-dimensional structure of catalase from Enterococcus faecalis. Acta Crystallogr D Biol Crystallogr, 60, 1374-1380. PubMed id: 15272159 DOI: 10.1107/S0907444904012004
28-Feb-04     Release date:   04-May-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q834P5  (Q834P5_ENTFA) -  Catalase
478 a.a.
474 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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+)
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     5 terms  


DOI no: 10.1107/S0907444904012004 Acta Crystallogr D Biol Crystallogr 60:1374-1380 (2004)
PubMed id: 15272159  
The three-dimensional structure of catalase from Enterococcus faecalis.
K.O.Håkansson, M.Brugna, L.Tasse.
Enterococcus faecalis haem catalase was crystallized using lithium sulfate at neutral pH. The crystals belong to space group R3, with unit-cell parameters a = b = 236.9, c = 198.1 A. The three-dimensional structure was determined by molecular replacement using a subunit of the Proteus mirabilis catalase structure. It was refined against 2.3 A synchrotron data to a free R factor of 21.8%. Like other catalases, the E. faecalis catalase is a homotetramer with a fold and structure similar to those of its structurally closest relative P. mirabilis. The solvent structure in the active site is identical in the four subunits but differs from that found in other catalases. The structural consequences of the Ramachandran outlier Ser196 are discussed.
  Selected figure(s)  
Figure 4.
Figure 4 The active site of E. faecalis catalase, showing the proximal ligand Tyr337 and its hydrogen-bond partner Arg333, together with a number of planar side-chain groups stacked on or around the haem group.
Figure 5.
Figure 5 Schematic representation of selected hydrogen bonds around the Ramachandran outlier Ser196. The figure attempts to illustrate how the unusual main-chain conformation affects the interactions between the Phe194-Phe199 segment and the neighbouring -strand and their hydrogen bonds to the important residue Arg333. The O atom of Ser196 makes a van der Waals contact with the haem group and is hydrogen bonded to the backbone carbonyl group of Thr129 and to a water molecule. The unusual conformation of Ser196 contributes two hydrogen bonds to Arg333: one from His197 and another from a water molecule bound to the carbonyl oxygen of Gly195.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 1374-1380) copyright 2004.  
  Figures were selected by an automated process.  

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.  
18498226 M.Zamocky, P.G.Furtmüller, and C.Obinger (2008).
Evolution of catalases from bacteria to humans.
  Antioxid Redox Signal, 10, 1527-1548.  
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.  
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