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PDBsum entry 1nm0

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protein ligands links
Oxidoreductase PDB id
1nm0
Jmol
Contents
Protein chain
476 a.a. *
Ligands
SO4 ×6
HEM-FMT
GOL
Waters ×471
* Residue conservation analysis
PDB id:
1nm0
Name: Oxidoreductase
Title: Proteus mirabilis catalase in complex with formiate
Structure: Catalase. Chain: a. Ec: 1.11.1.6
Source: Proteus mirabilis. Organism_taxid: 584
Biol. unit: Tetramer (from PQS)
Resolution:
2.30Å     R-factor:   0.181     R-free:   0.211
Authors: P.Andreoletti,A.Pernoud,P.Gouet,H.M.Jouve
Key ref:
P.Andreoletti et al. (2003). Structural studies of Proteus mirabilis catalase in its ground state, oxidized state and in complex with formic acid. Acta Crystallogr D Biol Crystallogr, 59, 2163-2168. PubMed id: 14646074 DOI: 10.1107/S0907444903019620
Date:
08-Jan-03     Release date:   20-Jan-04    
PROCHECK
Go to PROCHECK summary
 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 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; Manganese
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
Manganese
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: 10.1107/S0907444903019620 Acta Crystallogr D Biol Crystallogr 59:2163-2168 (2003)
PubMed id: 14646074  
 
 
Structural studies of Proteus mirabilis catalase in its ground state, oxidized state and in complex with formic acid.
P.Andreoletti, A.Pernoud, G.Sainz, P.Gouet, H.M.Jouve.
 
  ABSTRACT  
 
The structure of Proteus mirabilis catalase in complex with an inhibitor, formic acid, has been solved at 2.3 A resolution. Formic acid is a key ligand of catalase because of its ability to react with the ferric enzyme, giving a high-spin iron complex. Alternatively, it can react with two transient oxidized intermediates of the enzymatic mechanism, compounds I and II. In this work, the structures of native P. mirabilis catalase (PMC) and compound I have also been determined at high resolution (2.0 and 2.5 A, respectively) from frozen crystals. Comparisons between these three PMC structures show that a water molecule present at a distance of 3.5 A from the haem iron in the resting state is absent in the formic acid complex, but reappears in compound I. In addition, movements of solvent molecules are observed during formation of compound I in a cavity located away from the active site, in which a glycerol molecule is replaced by a sulfate. These results give structural insights into the movement of solvent molecules, which may be important in the enzymatic reaction.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 Comparison of the active site of PMC in three different states using the 2F[o] - F[c] electron-density map. Haem and the fundamental residues His54 and Tyr337 are shown in ball-and-stick representation, with N atoms in cyan, O atoms in red, C atoms in yellow and the Fe atom in magenta. The electron-density map is coloured blue and is contoured at 1 . (a) Native PMC at 2 resolution. The distances between the O atom of the water molecule and N 2 of His54 and the Fe atom are 2.8 and 3.5 , respectively. (b) Formic acid complex at 2.3 resolution. The distances between the formic acid molecule and His54 N 2 and the Fe atom are 2.7 and 2.8 , respectively. (c) Compound I at 2.5 resolution. The distances from the O atom of the water molecule to His54 N 2 and to the oxoferryl group are 2.7 and 3.1 , respectively. This figure was drawn with BobScript (Esnouf, 1997[Esnouf, R. M. (1997). J. Mol. Graph. 15, 132-134.]).
 
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 2163-2168) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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