PDBsum entry 1f4j

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Oxidoreductase PDB id
Protein chain
479 a.a. *
HEM ×4
Waters ×1239
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Structure of tetragonal crystals of human erythrocyte catalase
Structure: Catalase. Chain: a, b, c, d. Fragment: intact but lacks the first and last exons. Ec:
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Cell: erythrocyte
Biol. unit: Tetramer (from PQS)
2.40Å     R-factor:   0.196     R-free:   0.244
Authors: M.K.Safo,F.N.Musayev,S.H.Wu,D.J.Abraham,T.P.Ko
Key ref:
M.K.Safo et al. (2001). Structure of tetragonal crystals of human erythrocyte catalase. Acta Crystallogr D Biol Crystallogr, 57, 1-7. PubMed id: 11134921 DOI: 10.1107/S0907444900013767
07-Jun-00     Release date:   21-Jun-00    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P04040  (CATA_HUMAN) -  Catalase
527 a.a.
479 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 95.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   13 terms 
  Biological process     small molecule metabolic process   29 terms 
  Biochemical function     antioxidant activity     12 terms  


DOI no: 10.1107/S0907444900013767 Acta Crystallogr D Biol Crystallogr 57:1-7 (2001)
PubMed id: 11134921  
Structure of tetragonal crystals of human erythrocyte catalase.
M.K.Safo, F.N.Musayev, S.H.Wu, D.J.Abraham, T.P.Ko.
The structure of catalase from human erythrocytes (HEC) was determined in tetragonal crystals of space group I4(1) by molecular-replacement methods, using the orthorhombic crystal structure as a search model. It was then refined in a unit cell of dimensions a = b = 203.6 and c = 144.6 A, yielding R and R(free) of 0.196 and 0.244, respectively, for all data at 2.4 A resolution. A major difference of the HEC structure in the tetragonal crystal compared with the orthorhombic structure was the omission of a 20-residue N-terminal segment corresponding to the first exon of the human catalase gene. The overall structures were otherwise identical in both crystal forms. The NADPH-binding sites were empty in all four subunits and bound water molecules were observed at the active sites. The structure of the C-terminal segment, which corresponds to the last exon, remained undetermined. The tetragonal crystals showed a pseudo-4(1)22 symmetry in molecular packing. Two similar types of lattice contact interfaces between the HEC tetramers were observed; they were related by the pseudo-dyad axes.
  Selected figure(s)  
Figure 1.
Figure 1 Comparison of catalase structures from different organisms. The subunit models of (a) HEC and BLC, shown in orange and red, respectively, (b) HPII and PVC, in green and cyan, respectively, (c) SCCA and PMC, in magenta and blue, respectively, and (d) all six catalases were superimposed by O and the protein backbones were drawn using GRASP. The heme group is shown in red. NADPH is not shown. The position of Lys23 in HEC is indicated by an arrow in (a).
Figure 2.
Figure 2 Difference Fourier (2F[o] - F[c]) maps of the four heme groups in the tetragonal HEC crystal. Maps were calculated using the final model and contoured at 1.0 level, colored cyan. The heme groups of subunits A, B, C and D are shown in (a), (b), (c) and (d), respectively, with bonds in pink. Also shown are the residues His75, Asn148, Arg354 and Tyr358, as well as one or two active-site water molecules, colored green. The figures were produced using BobScript and Raster3D.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1-7) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18722522 Z.He, S.Yu, G.Mei, M.Zheng, M.Wang, Y.Dai, B.Tang, and N.Li (2008).
Maternally transmitted milk containing recombinant human catalase provides protection against oxidation for mouse offspring during lactation.
  Free Radic Biol Med, 45, 1135-1142.  
11496149 N.G.Milton, N.P.Mayor, and J.Rawlinson (2001).
Identification of amyloid-beta binding sites using an antisense peptide approach.
  Neuroreport, 12, 2561-2566.  
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.