spacer
spacer

PDBsum entry 1p7z

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1p7z
Jmol
Contents
Protein chains
727 a.a. *
Ligands
HEM ×4
Waters ×2733
* Residue conservation analysis
PDB id:
1p7z
Name: Oxidoreductase
Title: Crystal structure of the d181s variant of catalase hpii from e. Coli
Structure: Catalase hpii. Chain: a, b, c, d. Synonym: hydroxyperoxidase ii. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: kate. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.21Å     R-factor:   0.148     R-free:   0.211
Authors: P.Chelikani,X.Carpena,I.Fita,P.C.Loewen
Key ref:
P.Chelikani et al. (2003). An electrical potential in the access channel of catalases enhances catalysis. J Biol Chem, 278, 31290-31296. PubMed id: 12777389 DOI: 10.1074/jbc.M304076200
Date:
06-May-03     Release date:   09-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P21179  (CATE_ECOLI) -  Catalase HPII
Seq:
Struc:
 
Seq:
Struc:
753 a.a.
727 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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   2 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M304076200 J Biol Chem 278:31290-31296 (2003)
PubMed id: 12777389  
 
 
An electrical potential in the access channel of catalases enhances catalysis.
P.Chelikani, X.Carpena, I.Fita, P.C.Loewen.
 
  ABSTRACT  
 
Substrate H2O2 must gain access to the deeply buried active site of catalases through channels of 30-50 A in length. The most prominent or main channel approaches the active site perpendicular to the plane of the heme and contains a number of residues that are conserved in all catalases. Changes in Val169, 8 A from the heme in catalase HPII from Escherichia coli, introducing smaller, larger or polar side chains reduces the catalase activity. Changes in Asp181, 12 A from the heme, reduces activity by up to 90% if the negatively charged side chain is removed when Ala, Gln, Ser, Asn, or Ile are the substituted residues. Only the D181E variant retains wild type activity. Determination of the crystal structures of the Glu181, Ala181, Ser181, and Gln181 variants of HPII reveals lower water occupancy in the main channel of the less active variants, particularly at the position forming the sixth ligand to the heme iron and in the hydrophobic, constricted region adjacent to Val169. It is proposed that an electrical potential exists between the negatively charged aspartate (or glutamate) side chain at position 181 and the positively charged heme iron 12 A distant. The potential field acts upon the electrical dipoles of water generating a common orientation that favors hydrogen bond formation and promotes interaction with the heme iron. Substrate hydrogen peroxide would be affected similarly and would enter the active site oriented optimally for interaction with active site residues.
 
  Selected figure(s)  
 
Figure 3.
FIG. 3. a, schematic showing the distances among waters in the main channel of the D181E variant. The potential hydrogen bonds are shown as dashed lines, and the distances are expressed in Å. The water numbering is as in Fig. 2 and Table IV. b, stereo view oriented down the main channel toward the heme from Asp181. The slightly shifted location of the Glu side chain in the D181E variant is indicated in green. The water numbering is as in a.
Figure 4.
FIG. 4. Schematic of the main channel illustrating the presence of a negative charge (in green) on the side chain of Glu181 and a positive charge (in green) on the heme iron and the effect of the electrical potential between these two charges on the electrical dipoles of water in the channel and active site. The orientation of the electrical dipoles is indicated by the green arrow over each H[2]O. The location of the water molecules are those in subunit A of variant D181E.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 31290-31296) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20716293 D.E.Heck, M.Shakarjian, H.D.Kim, J.D.Laskin, and A.M.Vetrano (2010).
Mechanisms of oxidant generation by catalase.
  Ann N Y Acad Sci, 1203, 120-125.  
18498226 M.Zamocky, P.G.Furtmüller, and C.Obinger (2008).
Evolution of catalases from bacteria to humans.
  Antioxid Redox Signal, 10, 1527-1548.  
18425770 Z.Radisavljevic (2008).
AKT as locus of fragility in robust cancer system.
  J Cell Biochem, 104, 2071-2077.  
17158050 H.N.Kirkman, and G.F.Gaetani (2007).
Mammalian catalase: a venerable enzyme with new mysteries.
  Trends Biochem Sci, 32, 44-50.  
17063492 T.Deemagarn, B.Wiseman, X.Carpena, A.Ivancich, I.Fita, and P.C.Loewen (2007).
Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei.
  Proteins, 66, 219-228.
PDB codes: 2dv1 2dv2
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.  
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.