spacer
spacer

PDBsum entry 3ej6

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
3ej6
Jmol
Contents
Protein chains
681 a.a. *
Ligands
NAG ×8
HEM ×4
Waters ×1365
* Residue conservation analysis
PDB id:
3ej6
Name: Oxidoreductase
Title: Neurospora crassa catalase-3 crystal structure
Structure: Catalase-3. Chain: a, b, c, d. Ec: 1.11.1.6
Source: Neurospora crassa. Organism_taxid: 5141. Strain: 74-ors23-1a. Other_details: aerial mycelium
Resolution:
2.30Å     R-factor:   0.237     R-free:   0.242
Authors: A.Diaz,V.-J.Valdes,E.Rudino-Pinera,E.Horjales,W.Hansberg
Key ref:
A.Díaz et al. (2009). Structure-function relationships in fungal large-subunit catalases. J Mol Biol, 386, 218-232. PubMed id: 19109972 DOI: 10.1016/j.jmb.2008.12.019
Date:
17-Sep-08     Release date:   13-Jan-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9C169  (CAT3_NEUCR) -  Catalase-3
Seq:
Struc:
 
Seq:
Struc:
719 a.a.
681 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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 95.45% similarity
Mn(2+)
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  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2008.12.019 J Mol Biol 386:218-232 (2009)
PubMed id: 19109972  
 
 
Structure-function relationships in fungal large-subunit catalases.
A.Díaz, V.J.Valdés, E.Rudiño-Piñera, E.Horjales, W.Hansberg.
 
  ABSTRACT  
 
Neurospora crassa has two large-subunit catalases, CAT-1 and CAT-3. CAT-1 is associated with non-growing cells and accumulates particularly in asexual spores; CAT-3 is associated with growing cells and is induced under different stress conditions. It is our interest to elucidate the structure-function relationships in large-subunit catalases. Here we have determined the CAT-3 crystal structure and compared it with the previously determined CAT-1 structure. Similar to CAT-1, CAT-3 hydrogen peroxide (H(2)O(2)) saturation kinetics exhibited two components, consistent with the existence of two active sites: one saturated in the millimolar range and the other in the molar range. In the CAT-1 structure, we found three interesting features related to its unusual kinetics: (a) a constriction in the channel that conveys H(2)O(2) to the active site; (b) a covalent bond between the tyrosine, which forms the fifth coordination bound to the iron of the heme, and a vicinal cysteine; (c) oxidation of the pyrrole ring III to form a cis-hydroxyl group in C5 and a cis-gamma-spirolactone in C6. The site of heme oxidation marks the starts of the central channel that communicates to the central cavity and the shortest way products can exit the active site. CAT-3 has a similar constriction in its major channel, which could function as a gating system regulated by the H(2)O(2) concentration before the gate. CAT-3 functional tyrosine is not covalently bonded, but has instead the electron relay mechanism described for the human catalase to divert electrons from it. Pyrrole ring III in CAT-3 is not oxidized as it is in other large-subunit catalases whose structure has been determined. Different in CAT-3 from these enzymes is an occupied central cavity. Results presented here indicate that CAT-3 and CAT-1 enzymes represent a functional group of catalases with distinctive structural characteristics that determine similar kinetics.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Main-chain superposition of CAT-3, CAT-1, and PVC. (a) Stereo view of the monomer: CAT-3 in red, CAT-1 in blue, and PVC in green. (b) Stereo view of the carboxy-terminal domain: CAT-3 in red, CAT-1 in blue, and PVC in green.
Figure 6.
Fig. 6. CAT-3 active site compared to PVC and CAT-1. (a) Stereo view of the CAT-3 active site. Water molecules are shown in blue. Amino acids of a possible electron relay at the proximal side of the heme are shown. (b) Electronic density of the heme, water molecules, and interacting amino acid residues. (c) Comparison of CAT-3 non-oxidized heme with the oxidized one of PVC and amino acids from the proximal side. Instead of the CAT-3 Ser364, PVC (in red) has a methionine that displaces the equivalent His397 in CAT-3 (in green). Arg396 position also differs from the equivalent in PVC. (d) Comparison of CAT-3 non-oxidized heme with the oxidized one of CAT-1 and amino acids from the proximal side. Instead of a cysteine that makes a covalent bond with the active tyrosine in CAT-1 (in yellow), CAT-3 has Gln366 that is oriented away from the Tyr389. Compared to CAT-1, Tyr389 is also oriented differently and so is Arg396.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 386, 218-232) copyright 2009.  
  Figures were selected by an automated process.