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PDBsum entry 1sy7

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1sy7
Jmol PyMol
Contents
Protein chains
698 a.a. *
Ligands
HDD ×2
HEM ×2
Waters ×1725
* Residue conservation analysis
PDB id:
1sy7
Name: Oxidoreductase
Title: Crystal structure of the catalase-1 from neurospora crassa, structure at 1.75a resolution.
Structure: Catalase 1. Chain: a, b. Ec: 1.11.1.6
Source: Neurospora crassa. Organism_taxid: 5141. Strain: 74-ors23-1a
Biol. unit: Tetramer (from PDB file)
Resolution:
1.75Å     R-factor:   0.183     R-free:   0.206
Authors: A.Diaz,E.Horjales,E.Rudino-Pinera,R.Arreola,W.Hansberg
Key ref:
A.Díaz et al. (2004). Unusual Cys-Tyr covalent bond in a large catalase. J Mol Biol, 342, 971-985. PubMed id: 15342250 DOI: 10.1016/j.jmb.2004.07.027
Date:
01-Apr-04     Release date:   12-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9C168  (CAT1_NEUCR) -  Catalase-1
Seq:
Struc:
 
Seq:
Struc:
736 a.a.
698 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 = HDD) matches with 93.33% similarity
Mn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   4 terms 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2004.07.027 J Mol Biol 342:971-985 (2004)
PubMed id: 15342250  
 
 
Unusual Cys-Tyr covalent bond in a large catalase.
A.Díaz, E.Horjales, E.Rudiño-Piñera, R.Arreola, W.Hansberg.
 
  ABSTRACT  
 
Catalase-1, one of four catalase activities of Neurospora crassa, is associated with non-growing cells and accumulates in asexual spores. It is a large, tetrameric, highly efficient, and durable enzyme that is active even at molar concentrations of hydrogen peroxide. Catalase-1 is oxidized at the heme by singlet oxygen without significant effects on enzyme activity. Here we present the crystal structure of catalase-1 at 1.75A resolution. Compared to structures of other catalases of the large class, the main differences were found at the carboxy-terminal domain. The heme group is rotated 180 degrees around the alpha-gamma-meso carbon axis with respect to clade 3 small catalases. There is no co-ordination bond of the ferric ion at the heme distal side in catalase-1. The catalase-1 structure exhibited partial oxidation of heme b to heme d. Singlet oxygen, produced catalytically or by photosensitization, may hydroxylate C5 and C6 of pyrrole ring III with a subsequent formation of a gamma-spirolactone in C6. The modification site in catalases depends on the way dioxygen exits the protein: mainly through the central channel or the main channel in large and small catalases, respectively. The catalase-1 structure revealed an unusual covalent bond between a cysteine sulphur atom and the essential tyrosine residue of the proximal side of the active site. A peptide with the predicted theoretical mass of the two bound tryptic peptides was detected by mass spectrometry. A mechanism for the Cys-Tyr covalent bond formation is proposed. The tyrosine bound to the cysteine residue would be less prone to donate electrons to compound I to form compound II, explaining catalase-1 resistance to substrate inhibition and inactivation. An apparent constriction of the main channel at Ser198 lead us to propose a gate that opens the narrow part of the channel when there is sufficient hydrogen peroxide in the small cavity before the gate. This mechanism would explain the increase in catalytic velocity as the hydrogen peroxide concentration rises.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Proposed mechanism for the origin of the Cys-Tyr covalent bond. The mechanism requires enzyme activity. A tyrosine radical is reduced by the vicinal Cys356 forming a thiyl radical that induces deprotonation of the Tyr379 b-carbon atom and formation of the covalent bond.
Figure 7.
Figure 7. Channels in CAT-1. Shown are the water molecules and some of the residues that line the major channel, the lateral channel, and the central channel. The lateral channel starts about 14 Å from the proximal side of the heme. Only the first three water molecules of the central channel are shown, the second three are already in the central cavity. Heme is a superposition of the heme b and heme d models. Water molecules have a radius of 1.4 Å.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 971-985) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20936199 V.L.Davidson (2011).
Generation of protein-derived redox cofactors by posttranslational modification.
  Mol Biosyst, 7, 29-37.  
19897569 R.F.Chagas, A.M.Bailão, K.F.Fernandes, M.S.Winters, M.Pereira, and C.M.Soares (2010).
Purification of Paracoccidioides brasiliensis catalase P: subsequent kinetic and stability studies.
  J Biochem, 147, 345-351.  
18498226 M.Zamocky, P.G.Furtmüller, and C.Obinger (2008).
Evolution of catalases from bacteria to humans.
  Antioxid Redox Signal, 10, 1527-1548.  
17218317 H.Ouellet, K.Ranguelova, M.Labarre, J.B.Wittenberg, B.A.Wittenberg, R.S.Magliozzo, and M.Guertin (2007).
Reaction of Mycobacterium tuberculosis truncated hemoglobin O with hydrogen peroxide: evidence for peroxidatic activity and formation of protein-based radicals.
  J Biol Chem, 282, 7491-7503.  
17077971 N.Wang, Y.Yoshida, and K.Hasunuma (2007).
Loss of Catalase-1 (Cat-1) results in decreased conidial viability enhanced by exposure to light in Neurospora crassa.
  Mol Genet Genomics, 277, 13-22.  
17636331 N.Wang, Y.Yoshida, and K.Hasunuma (2007).
Catalase-1 (CAT-1) and nucleoside diphosphate kinase-1 (NDK-1) play an important role in protecting conidial viability under light stress in Neurospora crassa.
  Mol Genet Genomics, 278, 235-242.  
17188362 S.M.Kapetanaki, X.Zhao, S.Yu, R.S.Magliozzo, and J.P.Schelvis (2007).
Modification of the active site of Mycobacterium tuberculosis KatG after disruption of the Met-Tyr-Trp cross-linked adduct.
  J Inorg Biochem, 101, 422-433.  
17257049 Y.Wei, D.Ringe, M.A.Wilson, and M.J.Ondrechen (2007).
Identification of functional subclasses in the DJ-1 superfamily proteins.
  PLoS Comput Biol, 3, e10.  
15840564 R.A.Ghiladi, G.M.Knudsen, K.F.Medzihradszky, and P.R.Ortiz de Montellano (2005).
The Met-Tyr-Trp cross-link in Mycobacterium tuberculosis catalase-peroxidase (KatG): autocatalytic formation and effect on enzyme catalysis and spectroscopic properties.
  J Biol Chem, 280, 22651-22663.  
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.

 

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