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P0AB83

- END3_ECOLI

UniProt

P0AB83 - END3_ECOLI

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Protein
Endonuclease III
Gene
nth, b1633, JW1625
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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.3 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.1 Publication

Cofactori

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.2 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 N-glycosylase activity Source: UniProtKB-HAMAP
  3. DNA binding Source: UniProtKB-HAMAP
  4. DNA-(apurinic or apyrimidinic site) lyase activity Source: UniProtKB-HAMAP
  5. metal ion binding Source: UniProtKB-KW
  6. protein binding Source: IntAct

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 III (EC:4.2.99.18)
Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyase
Gene namesi
Name:nth
Ordered Locus Names:b1633, JW1625
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: 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 IIIUniRule annotation
PRO_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

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2ABKX-ray1.85A1-211[»]
ProteinModelPortaliP0AB83.

Miscellaneous databases

EvolutionaryTraceiP0AB83.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini108 – 12720HhH
Add
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0177.
HOGENOMiHOG000252206.
KOiK10773.
OMAiDTHIYRV.
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

MNKAKRLEIL TRLRENNPHP TTELNFSSPF ELLIAVLLSA QATDVSVNKA    50
TAKLYPVANT PAAMLELGVE GVKTYIKTIG LYNSKAENII KTCRILLEQH 100
NGEVPEDRAA LEALPGVGRK TANVVLNTAF GWPTIAVDTH IFRVCNRTQF 150
APGKNVEQVE EKLLKVVPAE FKVDCHHWLI LHGRYTCIAR KPRCGSCIIE 200
DLCEYKEKVD I 211
Length:211
Mass (Da):23,562
Last modified:November 8, 2005 - v1
Checksum:iFF4245823B7F902B
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
J02857 Genomic DNA. Translation: AAA24227.1 .
U00096 Genomic DNA. Translation: AAC74705.1 .
AP009048 Genomic DNA. Translation: BAA15387.1 .
PIRi A32412.
RefSeqi NP_416150.1. NC_000913.3.
YP_489897.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2ABK X-ray 1.85 A 1-211 [» ]
ProteinModelPortali P0AB83.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-48071N.
IntActi P0AB83. 6 interactions.
MINTi MINT-1223379.
STRINGi 511145.b1633.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC74705 ; AAC74705 ; b1633 .
BAA15387 ; BAA15387 ; BAA15387 .
GeneIDi 12933192.
947122.
KEGGi ecj:Y75_p1610.
eco:b1633.
PATRICi 32118568. VBIEscCol129921_1704.

Organism-specific databases

EchoBASEi EB0656.
EcoGenei EG10662. nth.

Phylogenomic databases

eggNOGi COG0177.
HOGENOMi HOG000252206.
KOi K10773.
OMAi DTHIYRV.
OrthoDBi EOG6H4KC5.
PhylomeDBi P0AB83.

Enzyme and pathway databases

BioCyci EcoCyc:EG10662-MONOMER.
ECOL316407:JW1625-MONOMER.
MetaCyc:EG10662-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0AB83.
PROi P0AB83.

Gene expression databases

Genevestigatori P0AB83.

Family and domain databases

Gene3Di 1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPi MF_00942. Nth.
InterProi IPR011257. 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 ]
Pfami PF10576. EndIII_4Fe-2S. 1 hit.
PF00633. HHH. 1 hit.
PF00730. HhH-GPD. 1 hit.
[Graphical view ]
PIRSFi PIRSF001435. Nth. 1 hit.
SMARTi SM00478. ENDO3c. 1 hit.
SM00525. FES. 1 hit.
SM00278. HhH1. 1 hit.
[Graphical view ]
SUPFAMi SSF48150. SSF48150. 1 hit.
TIGRFAMsi TIGR01083. nth. 1 hit.
PROSITEi PS00764. ENDONUCLEASE_III_1. 1 hit.
PS01155. ENDONUCLEASE_III_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

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(1989) [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(2006) [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(1984) [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(1988) [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(1994) [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(1992) [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(1995) [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 8, 2005
Last sequence update: November 8, 2005
Last modified: September 3, 2014
This is version 89 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

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