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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi187 – 1871Iron-sulfur (4Fe-4S)
Metal bindingi194 – 1941Iron-sulfur (4Fe-4S)
Metal bindingi197 – 1971Iron-sulfur (4Fe-4S)
Metal bindingi203 – 2031Iron-sulfur (4Fe-4S)

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-HAMAP
  2. DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB-HAMAP
  3. DNA binding Source: UniProtKB-HAMAP
  4. DNA N-glycosylase activity Source: UniProtKB-HAMAP
  5. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. base-excision repair Source: InterPro
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10662. nth.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi120 – 1201K → Q: 100000-fold decrease in activity and slight decrease in substrate affinity. 1 Publication
Mutagenesisi138 – 1381D → N: 100-fold decrease in activity and 4-fold increase in substrate affinity. 1 Publication
Mutagenesisi191 – 1911K → E: Slight decrease in activity and 130-fold increase in substrate affinity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 211211Endonuclease IIIPRO_0000102210Add
BLAST

Expressioni

Gene expression databases

GenevestigatoriP0AB83.

Interactioni

Subunit structurei

Monomer.1 Publication

Binary interactionsi

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

Protein-protein interaction databases

DIPiDIP-48071N.
IntActiP0AB83. 6 interactions.
MINTiMINT-1223379.
STRINGi511145.b1633.

Structurei

Secondary structure

1
211
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1614Combined sources
Helixi29 – 3810Combined sources
Turni39 – 413Combined sources
Helixi44 – 5411Combined sources
Turni55 – 573Combined sources
Helixi61 – 7616Combined sources
Helixi82 – 9817Combined sources
Turni99 – 1024Combined sources
Helixi108 – 1136Combined sources
Helixi119 – 13012Combined sources
Helixi139 – 14810Combined sources
Helixi156 – 16611Combined sources
Helixi169 – 1713Combined sources
Turni172 – 1743Combined sources
Helixi175 – 18511Combined sources
Beta strandi189 – 1913Combined sources
Helixi194 – 1963Combined sources
Helixi200 – 2023Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ABKX-ray1.85A1-211[»]
SMRiP0AB83. Positions 1-211.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AB83.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini108 – 12720HhHUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0177.
HOGENOMiHOG000252206.
InParanoidiP0AB83.
KOiK10773.
OMAiNNKSKHL.
OrthoDBiEOG6H4KC5.
PhylomeDBiP0AB83.

Family and domain databases

Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPiMF_00942. Nth.
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.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_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.
SM00278. HhH1. 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 7, 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.
YP_489897.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74705; AAC74705; b1633.
BAA15387; BAA15387; BAA15387.
GeneIDi12933192.
947122.
KEGGiecj:Y75_p1610.
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.
YP_489897.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ABKX-ray1.85A1-211[»]
SMRiP0AB83. Positions 1-211.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48071N.
IntActiP0AB83. 6 interactions.
MINTiMINT-1223379.
STRINGi511145.b1633.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74705; AAC74705; b1633.
BAA15387; BAA15387; BAA15387.
GeneIDi12933192.
947122.
KEGGiecj:Y75_p1610.
eco:b1633.
PATRICi32118568. VBIEscCol129921_1704.

Organism-specific databases

EchoBASEiEB0656.
EcoGeneiEG10662. nth.

Phylogenomic databases

eggNOGiCOG0177.
HOGENOMiHOG000252206.
InParanoidiP0AB83.
KOiK10773.
OMAiNNKSKHL.
OrthoDBiEOG6H4KC5.
PhylomeDBiP0AB83.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP0AB83.
PROiP0AB83.

Gene expression databases

GenevestigatoriP0AB83.

Family and domain databases

Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPiMF_00942. Nth.
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.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_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.
SM00278. HhH1. 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...

Publicationsi

« Hide 'large scale' publications
  1. "Purification and characterization of Escherichia coli endonuclease III from the cloned nth gene."
    Asahara H., Wistort P.M., Bank J.F., Bakerian R.H., Cunningham R.P.
    Biochemistry 28:4444-4449(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10, FUNCTION.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "DNA glycosylase activities for thymine residues damaged by ring saturation, fragmentation, or ring contraction are functions of endonuclease III in Escherichia coli."
    Breimer L.H., Lindahl T.
    J. Biol. Chem. 259:5543-5548(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT.
  6. "The mechanisms of action of E. coli endonuclease III and T4 UV endonuclease (endonuclease V) at AP sites."
    Kim J., Linn S.
    Nucleic Acids Res. 16:1135-1141(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  7. "Structure and function of Escherichia coli endonuclease III."
    Cunningham R.P., Ahern H., Xing D., Thayer M.M., Tainer J.A.
    Ann. N. Y. Acad. Sci. 726:215-222(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: COFACTOR.
  8. "Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III."
    Kuo C.-F., McRee D., Fisher C.L., O'Handley S.F., Cunningham R.P., Tainer J.A.
    Science 258:434-440(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
  9. "Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure."
    Thayer M.M., Ahern H., Xing D., Cunningham R.P., Tainer J.A.
    EMBO J. 14:4108-4120(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), COFACTOR, DNA-BINDING, MUTAGENESIS OF LYS-120; ASP-138 AND LYS-191.

Entry informationi

Entry nameiEND3_ECOLI
AccessioniPrimary (citable) accession number: P0AB83
Secondary accession number(s): P20625
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 7, 2005
Last sequence update: November 7, 2005
Last modified: March 31, 2015
This is version 94 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

External Data

Dasty 3

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 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.