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PDBsum entry 6ri4

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protein ligands metals links
Oxidoreductase PDB id
6ri4

 

 

 

 

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Contents
Protein chain
498 a.a.
Ligands
NAG-NAG
NAG-NAG-BMA
OXY
Metals
_CU ×4
__F
Waters ×914
PDB id:
6ri4
Name: Oxidoreductase
Title: Single crystal serial study of the inhibition of laccases from steccherinum murashkinskyi by fluoride anions at sub-atomic resolution. First structure of the series with 13 kgy dose.
Structure: Laccase 2. Chain: a. Ec: 1.10.3.2
Source: Steccherinum murashkinskyi. Organism_taxid: 627145
Resolution:
1.08Å     R-factor:   0.131     R-free:   0.152
Authors: K.M.Polyakov,S.Gavryushov,T.V.Fedorova,O.A.Glazunova,A.N.Popov
Key ref: K.M.Polyakov et al. (2019). The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism. Acta Crystallogr D Struct Biol, 75, 804-816. PubMed id: 31478903 DOI: 10.1107/S2059798319010684
Date:
23-Apr-19     Release date:   01-May-19    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
I1VE66  (I1VE66_9APHY) -  laccase from Metuloidea murashkinskyi
Seq:
Struc:
 
Seq:
Struc:
546 a.a.
498 a.a.
Key:    Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.1.10.3.2  - laccase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 hydroquinone + O2 = 4 benzosemiquinone + 2 H2O
4 × hydroquinone
+
O2
Bound ligand (Het Group name = OXY)
corresponds exactly
= 4 × benzosemiquinone
+ 2 × H2O
      Cofactor: Cu cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1107/S2059798319010684 Acta Crystallogr D Struct Biol 75:804-816 (2019)
PubMed id: 31478903  
 
 
The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism.
K.M.Polyakov, S.Gavryushov, T.V.Fedorova, O.A.Glazunova, A.N.Popov.
 
  ABSTRACT  
 
Laccases are enzymes that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of molecular oxygen to water. Here, a subatomic resolution X-ray crystallographic study of the mechanism of inhibition of the laccase from the basidiomycete fungus Steccherinum murashkinskyi by chloride and fluoride ions is presented. Three series of X-ray diffraction data sets were collected with increasing doses of absorbed X-ray radiation from a native S. murashkinskyi laccase crystal and from crystals of complexes of the laccase with chloride and fluoride ions. The data for the native laccase crystal confirmed the previously deduced enzymatic mechanism of molecular oxygen reduction. The structures of the complexes allowed the localization of chloride and fluoride ions in the channel near the T2 copper ion. These ions replace the oxygen ligand of the T2 copper ion in this channel and can play the role of this ligand in the enzymatic reaction. As follows from analysis of the structures from the increasing dose series, the inhibition of laccases by chloride and fluoride anions can be explained by the fact that the binding of these negatively charged ions at the position of the oxygen ligand of the T2 copper ion impedes the reduction of the T2 copper ion.
 

 

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