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HAMAP rule MF_03183

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General rule information [?]

Accession MF_03183
Dates 6-MAR-2014 (Created)
19-NOV-2022 (Last updated, Version 13)
Name Endonuclease_III_Nth
Scope(s) Eukaryota
Template(s) P78549 (NTH_HUMAN); P31378 (NTH1_YEAST); Q08214 (NTH2_YEAST); Q09907 (NTH_SCHPO); [ Recover all ]
Triggered by HAMAP; MF_03183 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier NTH
case <OC:Vertebrata>
Protein name RecName: Full=Endonuclease III-like protein 1;
                 EC=3.2.2.-;
                 EC=4.2.99.18;
AltName: Full=Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
                 Short=DNA glycosylase/AP lyase;
else
Protein name RecName: Full=Endonuclease III homolog;
                 EC=3.2.2.-;
                 EC=4.2.99.18;
AltName: Full=Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase;
                 Short=DNA glycosylase/AP lyase;
end case
case <OC:Vertebrata>
Gene name Name=NTHL1;
else case <OC:Caenorhabditis>
Gene name Name=nth-1;
else case <OC:Saccharomycotina>
Gene name Name=NTG1;
else
Gene name Name=NTH1;
end case

Comments [?]

FUNCTIONBifunctional DNA N-glycosylase with associated apurinic/apyrimidinic (AP) lyase function that catalyzes the first step in base excision repair (BER), the primary repair pathway for the repair of oxidative DNA damage. The DNA N-glycosylase activity releases the damaged DNA base from DNA by cleaving the N-glycosidic bond, leaving an AP site. The AP lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination. Primarily recognizes and repairs oxidative base damage of pyrimidines.
CATALYTIC ACTIVITY Reaction=2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'- deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho- 2'-deoxyribonucleoside-DNA + H(+); Xref=Rhea:RHEA:66592, Rhea:RHEA- COMP:13180, Rhea:RHEA-COMP:16897, Rhea:RHEA-COMP:17067, ChEBI:CHEBI:15378, ChEBI:CHEBI:136412, ChEBI:CHEBI:157695, ChEBI:CHEBI:167181; EC=4.2.99.18;
case <FTGroup:1>
COFACTOR Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Note=Binds 1 [4Fe-4S] cluster. The cluster does not appear to play a role in catalysis, but is probably involved in the proper positioning of the enzyme along the DNA strand.;
end case
case <OC:Mammalia>
SUBUNITInteracts with YBX1.
end case
case not <OC:Viridiplantae>
SUBCELLULAR LOCATIONNucleus. Mitochondrion.
end case
SIMILARITYBelongs to the Nth/MutY family.

Keywords [?]

DNA damage
DNA repair
Glycosidase
Hydrolase
Lyase
case not <OC:Viridiplantae>
Mitochondrion
Nucleus
end case
case <FTGroup:1>
4Fe-4S
Iron
Iron-sulfur
Metal-binding
end case

Gene Ontology [?]

case not <OCellular component:Viridiplantae>
GO:0005739; Cellular component:mitochondrion
GO:0005634; Cellular component:nucleus
end case
GO:0000703; Molecular function:oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
GO:0003906; Molecular function:DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0003677; Molecular function:DNA binding
case <FTGroup:1>
GO:0051539; Molecular function:4 iron, 4 sulfur cluster binding
end case
GO:0006285; Biological process:base-excision repair, AP site formation

Cross-references [?]

PROSITE PS01155; ENDONUCLEASE_III_2; 1;
PROSITE PS00764; ENDONUCLEASE_III_1; 1;
Pfam PF00633; HHH; 1;
Pfam PF00730; HhH-GPD; 1;
Pfam PF10576; EndIII_4Fe-2S; 1;
PIRSF PIRSF001435; Nth; 1;
General TransitM; -; 0-1;

Features [?]

From: NTH_HUMAN (P78549)
Key From To Description Tag Condition FTGroup
ACT_SITE 220 220 /note="Nucleophile; for N-glycosylase activity" K
BINDING 290 290 /ligand="[4Fe-4S] cluster"
/ligand_id="ChEBI:CHEBI:49883"
C 1
BINDING 297 297 /ligand="[4Fe-4S] cluster"
/ligand_id="ChEBI:CHEBI:49883"
C 1
BINDING 300 300 /ligand="[4Fe-4S] cluster"
/ligand_id="ChEBI:CHEBI:49883"
C 1
BINDING 306 306 /ligand="[4Fe-4S] cluster"
/ligand_id="ChEBI:CHEBI:49883"
C 1
SITE 239 239 /note="Important for catalytic activity" D

Additional information [?]

Size range 238-835 amino acids
Related rules None
Fusion Nter: None Cter: None



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