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Protein

Endonuclease III

Gene

nth

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.UniRule annotation3 Publications

Catalytic activityi

The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.UniRule annotation1 Publication

Cofactori

[4Fe-4S] clusterUniRule annotation2 PublicationsNote: Binds 1 [4Fe-4S] cluster. The cluster does not appear to play a role in catalysis, but is probably involved in DNA-binding and proper positioning of the enzyme along the DNA strand.UniRule annotation2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi187Iron-sulfur (4Fe-4S)Combined sources1 Publication1
Metal bindingi194Iron-sulfur (4Fe-4S)Combined sources1 Publication1
Metal bindingi197Iron-sulfur (4Fe-4S)Combined sources1 Publication1
Metal bindingi203Iron-sulfur (4Fe-4S)Combined sources1 Publication1

GO - Molecular functioni

  • 4 iron, 4 sulfur cluster binding Source: EcoCyc
  • DNA-(apurinic or apyrimidinic site) lyase activity Source: EcoCyc
  • DNA binding Source: UniProtKB-HAMAP
  • DNA N-glycosylase activity Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW
  • oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity Source: EcoCyc

GO - Biological processi

  • base-excision repair, AP site formation Source: EcoCyc
  • cellular response to UV Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase, Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

4Fe-4S, DNA-binding, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10662-MONOMER.
ECOL316407:JW1625-MONOMER.
MetaCyc:EG10662-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Endonuclease IIIUniRule annotation (EC:4.2.99.18UniRule annotation)
Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyaseUniRule annotation
Gene namesi
Name:nthUniRule annotation
Ordered Locus Names:b1633, JW1625
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10662. nth.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi120K → Q: 100000-fold decrease in activity and slight decrease in substrate affinity. 1 Publication1
Mutagenesisi138D → N: 100-fold decrease in activity and 4-fold increase in substrate affinity. 1 Publication1
Mutagenesisi191K → E: Slight decrease in activity and 130-fold increase in substrate affinity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001022101 – 211Endonuclease IIIAdd BLAST211

Proteomic databases

PaxDbiP0AB83.
PRIDEiP0AB83.

Interactioni

Subunit structurei

Monomer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
aceEP0AFG82EBI-555213,EBI-542683

Protein-protein interaction databases

BioGridi4262186. 123 interactors.
DIPiDIP-48071N.
IntActiP0AB83. 6 interactors.
MINTiMINT-1223379.
STRINGi511145.b1633.

Structurei

Secondary structure

1211
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 16Combined sources14
Helixi29 – 38Combined sources10
Turni39 – 41Combined sources3
Helixi44 – 54Combined sources11
Turni55 – 57Combined sources3
Helixi61 – 76Combined sources16
Helixi82 – 98Combined sources17
Turni99 – 102Combined sources4
Helixi108 – 113Combined sources6
Helixi119 – 130Combined sources12
Helixi139 – 148Combined sources10
Helixi156 – 166Combined sources11
Helixi169 – 171Combined sources3
Turni172 – 174Combined sources3
Helixi175 – 185Combined sources11
Beta strandi189 – 191Combined sources3
Helixi194 – 196Combined sources3
Helixi200 – 202Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2ABKX-ray1.85A1-211[»]
ProteinModelPortaliP0AB83.
SMRiP0AB83.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AB83.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini108 – 127HhHUniRule annotationAdd BLAST20

Sequence similaritiesi

Belongs to the Nth/MutY family.UniRule annotation
Contains 1 HhH domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CSM. Bacteria.
COG0177. LUCA.
HOGENOMiHOG000252206.
InParanoidiP0AB83.
KOiK10773.
OMAiYVCTARK.
PhylomeDBiP0AB83.

Family and domain databases

CDDicd00056. ENDO3c. 1 hit.
Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPiMF_00942. Nth. 1 hit.
InterProiIPR011257. DNA_glycosylase.
IPR004036. Endonuclease-III-like_CS2.
IPR004035. Endouclease-III_FeS-bd_BS.
IPR003651. Endouclease3_FeS-loop_motif.
IPR003265. HhH-GPD_domain.
IPR000445. HhH_motif.
IPR023170. HTH_base_excis_C.
IPR005759. Nth.
[Graphical view]
PfamiPF10576. EndIII_4Fe-2S. 1 hit.
PF00633. HHH. 1 hit.
PF00730. HhH-GPD. 1 hit.
[Graphical view]
PIRSFiPIRSF001435. Nth. 1 hit.
SMARTiSM00478. ENDO3c. 1 hit.
SM00525. FES. 1 hit.
[Graphical view]
SUPFAMiSSF48150. SSF48150. 1 hit.
TIGRFAMsiTIGR01083. nth. 1 hit.
PROSITEiPS00764. ENDONUCLEASE_III_1. 1 hit.
PS01155. ENDONUCLEASE_III_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0AB83-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNKAKRLEIL TRLRENNPHP TTELNFSSPF ELLIAVLLSA QATDVSVNKA
60 70 80 90 100
TAKLYPVANT PAAMLELGVE GVKTYIKTIG LYNSKAENII KTCRILLEQH
110 120 130 140 150
NGEVPEDRAA LEALPGVGRK TANVVLNTAF GWPTIAVDTH IFRVCNRTQF
160 170 180 190 200
APGKNVEQVE EKLLKVVPAE FKVDCHHWLI LHGRYTCIAR KPRCGSCIIE
210
DLCEYKEKVD I
Length:211
Mass (Da):23,562
Last modified:November 8, 2005 - v1
Checksum:iFF4245823B7F902B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02857 Genomic DNA. Translation: AAA24227.1.
U00096 Genomic DNA. Translation: AAC74705.1.
AP009048 Genomic DNA. Translation: BAA15387.1.
PIRiA32412.
RefSeqiNP_416150.1. NC_000913.3.
WP_001030339.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74705; AAC74705; b1633.
BAA15387; BAA15387; BAA15387.
GeneIDi947122.
KEGGiecj:JW1625.
eco:b1633.
PATRICi32118568. VBIEscCol129921_1704.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J02857 Genomic DNA. Translation: AAA24227.1.
U00096 Genomic DNA. Translation: AAC74705.1.
AP009048 Genomic DNA. Translation: BAA15387.1.
PIRiA32412.
RefSeqiNP_416150.1. NC_000913.3.
WP_001030339.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2ABKX-ray1.85A1-211[»]
ProteinModelPortaliP0AB83.
SMRiP0AB83.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262186. 123 interactors.
DIPiDIP-48071N.
IntActiP0AB83. 6 interactors.
MINTiMINT-1223379.
STRINGi511145.b1633.

Proteomic databases

PaxDbiP0AB83.
PRIDEiP0AB83.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74705; AAC74705; b1633.
BAA15387; BAA15387; BAA15387.
GeneIDi947122.
KEGGiecj:JW1625.
eco:b1633.
PATRICi32118568. VBIEscCol129921_1704.

Organism-specific databases

EchoBASEiEB0656.
EcoGeneiEG10662. nth.

Phylogenomic databases

eggNOGiENOG4105CSM. Bacteria.
COG0177. LUCA.
HOGENOMiHOG000252206.
InParanoidiP0AB83.
KOiK10773.
OMAiYVCTARK.
PhylomeDBiP0AB83.

Enzyme and pathway databases

BioCyciEcoCyc:EG10662-MONOMER.
ECOL316407:JW1625-MONOMER.
MetaCyc:EG10662-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AB83.
PROiP0AB83.

Family and domain databases

CDDicd00056. ENDO3c. 1 hit.
Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPiMF_00942. Nth. 1 hit.
InterProiIPR011257. DNA_glycosylase.
IPR004036. Endonuclease-III-like_CS2.
IPR004035. Endouclease-III_FeS-bd_BS.
IPR003651. Endouclease3_FeS-loop_motif.
IPR003265. HhH-GPD_domain.
IPR000445. HhH_motif.
IPR023170. HTH_base_excis_C.
IPR005759. Nth.
[Graphical view]
PfamiPF10576. EndIII_4Fe-2S. 1 hit.
PF00633. HHH. 1 hit.
PF00730. HhH-GPD. 1 hit.
[Graphical view]
PIRSFiPIRSF001435. Nth. 1 hit.
SMARTiSM00478. ENDO3c. 1 hit.
SM00525. FES. 1 hit.
[Graphical view]
SUPFAMiSSF48150. SSF48150. 1 hit.
TIGRFAMsiTIGR01083. nth. 1 hit.
PROSITEiPS00764. ENDONUCLEASE_III_1. 1 hit.
PS01155. ENDONUCLEASE_III_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiEND3_ECOLI
AccessioniPrimary (citable) accession number: P0AB83
Secondary accession number(s): P20625
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: November 8, 2005
Last modified: November 2, 2016
This is version 106 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.