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Protein

Endonuclease III homolog 2

Gene

NTG2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Bifunctional 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, but also purine-derived lesions, alkylation damage as well as abasic sites. Can also repair the oxidation products of 8-oxoguanine.UniRule annotation10 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 annotationNote: 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.UniRule annotation

Kineticsi

  1. KM=160 nM for dihydrouracil containing duplex oligonucleotides (N-glycosylase activity)3 Publications
  2. KM=178 nM for 5-hydroxy-6-hydrothymine containing duplex oligonucleotides (N-glycosylase activity)3 Publications
  3. KM=557 nM for 5-hydroxy-6-hydrouracil containing duplex oligonucleotides (N-glycosylase activity)3 Publications
  4. KM=431 nM for 5-hydroxyuracil containing duplex oligonucleotides (N-glycosylase activity)3 Publications
  5. KM=419 nM for 5-hydroxycytosine containing duplex oligonucleotides (N-glycosylase activity)3 Publications
  6. KM=1000 nM for thymine glycol containing duplex oligonucleotides (N-glycosylase activity)3 Publications
  7. KM=824 nM for 2,6-diamino-4-hydroxy-5-formamidopyrimidine FapyAde) containing duplex oligonucleotides (N-glycosylase activity)3 Publications
  8. KM=2529 nM for 4,6-diamino-5-formamidopyrimidine (FapyGua) containing duplex oligonucleotides (N-glycosylase activity)3 Publications
  1. Vmax=0.2 nmol/min/ng enzyme for dihydrouracil containing duplex oligonucleotides (N-glycosylase activity)3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei248 – 2481Nucleophile; for N-glycosylase activityUniRule annotation
Sitei267 – 2671Important for catalytic activityUniRule annotation
Metal bindingi319 – 3191Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi326 – 3261Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi329 – 3291Iron-sulfur (4Fe-4S)UniRule annotation
Metal bindingi335 – 3351Iron-sulfur (4Fe-4S)UniRule annotation

GO - Molecular functioni

GO - Biological processi

  • base-excision repair Source: SGD
  • base-excision repair, AP site formation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase, Lyase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciYEAST:G3O-33457-MONOMER.
ReactomeiR-SCE-110329. Cleavage of the damaged pyrimidine.
R-SCE-110357. Displacement of DNA glycosylase by APEX1.

Names & Taxonomyi

Protein namesi
Recommended name:
Endonuclease III homolog 2UniRule annotation (EC:3.2.2.-UniRule annotation, EC:4.2.99.18UniRule annotation)
Alternative name(s):
Bifunctional DNA N-glycoslyase/DNA-(apurinic or apyrimidinic site) lyase 2UniRule annotation
Short name:
DNA glycoslyase/AP lyase 2UniRule annotation
Endonuclease III-like glycosylase 2
Redoxyendonuclease 2
Gene namesi
Name:NTG2
Synonyms:SCR2
Ordered Locus Names:YOL043C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOL043C.
SGDiS000005403. NTG2.

Subcellular locationi

GO - Cellular componenti

  • mitochondrion Source: UniProtKB-HAMAP
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Greatly increases spontaneous and hydrogen peroxide-induced mutation frequency.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi24 – 241S → A: Abolishes interaction with MLH1. 1 Publication
Mutagenesisi26 – 261Y → A: Abolishes interaction with MLH1. 1 Publication
Mutagenesisi27 – 271F → A: Abolishes interaction with MLH1. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 380380Endonuclease III homolog 2PRO_0000102238Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki194 – 194Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)Sequence analysis

Post-translational modificationi

Monosumoylated.

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiQ08214.
TopDownProteomicsiQ08214.

Expressioni

Inductioni

Constitutively expressed.2 Publications

Interactioni

Subunit structurei

Interacts with MLH1.1 Publication

Protein-protein interaction databases

BioGridi34359. 46 interactions.
DIPiDIP-2956N.
IntActiQ08214. 1 interaction.
MINTiMINT-570318.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4FMNX-ray2.69C22-29[»]
ProteinModelPortaliQ08214.
SMRiQ08214. Positions 204-342.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini228 – 25225HhHUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni15 – 4026Interaction with MLH1Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi8 – 125Nuclear localization signalSequence analysis
Motifi376 – 3805Nuclear localization signalSequence analysis

Sequence similaritiesi

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

Phylogenomic databases

GeneTreeiENSGT00510000047513.
HOGENOMiHOG000252209.
InParanoidiQ08214.
KOiK10773.
OMAiLWYEINT.
OrthoDBiEOG7PK99N.

Family and domain databases

Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPiMF_03183. Endonuclease_III_Nth.
InterProiIPR011257. DNA_glycosylase.
IPR004036. Endonuclease-III-like_CS2.
IPR003651. Endouclease3_FeS-loop_motif.
IPR003265. HhH-GPD_domain.
IPR023170. HTH_base_excis_C.
IPR030841. NTH1.
[Graphical view]
PfamiPF00730. HhH-GPD. 1 hit.
[Graphical view]
SMARTiSM00478. ENDO3c. 1 hit.
SM00525. FES. 1 hit.
[Graphical view]
SUPFAMiSSF48150. SSF48150. 1 hit.
PROSITEiPS01155. ENDONUCLEASE_III_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q08214-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MREESRSRKR KHIPVDIEEV EVRSKYFKKN ERTVELVKEN KINKDLQNYG
60 70 80 90 100
GVNIDWIKAL KPIEYFEWIE SRTCDDPRTW GRPITKEEMI NDSGAKVPES
110 120 130 140 150
FLPIYNRVRL MRSKVKTPVD AMGCSMIPVL VSNKCGIPSE KVDPKNFRLQ
160 170 180 190 200
FLIGTMLSAQ TRDERMAQAA LNITEYCLNT LKIAEGITLD GLLKIDEPVL
210 220 230 240 250
ANLIRCVSFY TRKANFIKRT AQLLVDNFDS DIPYDIEGIL SLPGVGPKMG
260 270 280 290 300
YLTLQKGWGL IAGICVDVHV HRLCKMWNWV DPIKCKTAEH TRKELQVWLP
310 320 330 340 350
HSLWYEINTV LVGFGQLICM ARGKRCDLCL ANDVCNARNE KLIESSKFHQ
360 370 380
LEDKEDIEKV YSHWLDTVTN GITTERHKKK
Length:380
Mass (Da):43,844
Last modified:November 1, 1996 - v1
Checksum:i517F81C3BA3DDCF7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74785 Genomic DNA. Translation: CAA99045.1.
BK006948 Genomic DNA. Translation: DAA10739.1.
PIRiS66728.
RefSeqiNP_014599.1. NM_001183297.1.

Genome annotation databases

EnsemblFungiiYOL043C; YOL043C; YOL043C.
GeneIDi854114.
KEGGisce:YOL043C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z74785 Genomic DNA. Translation: CAA99045.1.
BK006948 Genomic DNA. Translation: DAA10739.1.
PIRiS66728.
RefSeqiNP_014599.1. NM_001183297.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4FMNX-ray2.69C22-29[»]
ProteinModelPortaliQ08214.
SMRiQ08214. Positions 204-342.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34359. 46 interactions.
DIPiDIP-2956N.
IntActiQ08214. 1 interaction.
MINTiMINT-570318.

Proteomic databases

MaxQBiQ08214.
TopDownProteomicsiQ08214.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOL043C; YOL043C; YOL043C.
GeneIDi854114.
KEGGisce:YOL043C.

Organism-specific databases

EuPathDBiFungiDB:YOL043C.
SGDiS000005403. NTG2.

Phylogenomic databases

GeneTreeiENSGT00510000047513.
HOGENOMiHOG000252209.
InParanoidiQ08214.
KOiK10773.
OMAiLWYEINT.
OrthoDBiEOG7PK99N.

Enzyme and pathway databases

BioCyciYEAST:G3O-33457-MONOMER.
ReactomeiR-SCE-110329. Cleavage of the damaged pyrimidine.
R-SCE-110357. Displacement of DNA glycosylase by APEX1.

Miscellaneous databases

PROiQ08214.

Family and domain databases

Gene3Di1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.
HAMAPiMF_03183. Endonuclease_III_Nth.
InterProiIPR011257. DNA_glycosylase.
IPR004036. Endonuclease-III-like_CS2.
IPR003651. Endouclease3_FeS-loop_motif.
IPR003265. HhH-GPD_domain.
IPR023170. HTH_base_excis_C.
IPR030841. NTH1.
[Graphical view]
PfamiPF00730. HhH-GPD. 1 hit.
[Graphical view]
SMARTiSM00478. ENDO3c. 1 hit.
SM00525. FES. 1 hit.
[Graphical view]
SUPFAMiSSF48150. SSF48150. 1 hit.
PROSITEiPS01155. ENDONUCLEASE_III_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
    Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
    , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
    Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "Purification, characterization, gene cloning, and expression of Saccharomyces cerevisiae redoxyendonuclease, a homolog of Escherichia coli endonuclease III."
    Augeri L., Lee Y.M., Barton A.B., Doetsch P.W.
    Biochemistry 36:721-729(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. "Saccharomyces cerevisiae possesses two functional homologues of Escherichia coli endonuclease III."
    You H.J., Swanson R.L., Doetsch P.W.
    Biochemistry 37:6033-6040(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBSTRATES, INDUCTION, BIOPHYSICOCHEMICAL PROPERTIES.
  5. "Substrate specificities of the ntg1 and ntg2 proteins of Saccharomyces cerevisiae for oxidized DNA bases are not identical."
    Senturker S., Auffret van der Kemp P., You H.J., Doetsch P.W., Dizdaroglu M., Boiteux S.
    Nucleic Acids Res. 26:5270-5276(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBSTRATES, BIOPHYSICOCHEMICAL PROPERTIES.
  6. "Saccharomyces cerevisiae Ntg1p and Ntg2p: broad specificity N-glycosylases for the repair of oxidative DNA damage in the nucleus and mitochondria."
    You H.J., Swanson R.L., Harrington C., Corbett A.H., Jinks-Robertson S., Sentuerker S., Wallace S.S., Boiteux S., Dizdaroglu M., Doetsch P.W.
    Biochemistry 38:11298-11306(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  7. "The Saccharomyces cerevisiae homologues of endonuclease III from Escherichia coli, Ntg1 and Ntg2, are both required for efficient repair of spontaneous and induced oxidative DNA damage in yeast."
    Alseth I., Eide L., Pirovano M., Rognes T., Seeberg E., Bjoras M.
    Mol. Cell. Biol. 19:3779-3787(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN OXIDATIVE DNA DAMAGE REPAIR, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE, INDUCTION.
  8. "Ntg2 of Saccharomyces cerevisiae repairs the oxidation products of 8-hydroxyguanine."
    Kim J.E., You H.J., Choi J.Y., Doetsch P.W., Kim J.S., Chung M.H.
    Biochem. Biophys. Res. Commun. 285:1186-1191(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  9. "Ntg2p, a Saccharomyces cerevisiae DNA N-glycosylase/apurinic or apyrimidinic lyase involved in base excision repair of oxidative DNA damage, interacts with the DNA mismatch repair protein Mlh1p. Identification of a Mlh1p binding motif."
    Gellon L., Werner M., Boiteux S.
    J. Biol. Chem. 277:29963-29972(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH MLH1, MUTAGENESIS OF SER-24; TYR-26 AND PHE-27.
  10. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  11. "Characterization of AP lyase activities of Saccharomyces cerevisiae Ntg1p and Ntg2p: implications for biological function."
    Meadows K.L., Song B., Doetsch P.W.
    Nucleic Acids Res. 31:5560-5567(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
  12. "Involvement of two endonuclease III homologs in the base excision repair pathway for the processing of DNA alkylation damage in Saccharomyces cerevisiae."
    Hanna M., Chow B.L., Morey N.J., Jinks-Robertson S., Doetsch P.W., Xiao W.
    DNA Repair 3:51-59(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN DNA ALKYLATION DAMAGE REPAIR.
  13. "Role of OGG1 and NTG2 in the repair of oxidative DNA damage and mutagenesis induced by hydrogen peroxide in Saccharomyces cerevisiae: relationships with transition metals iron and copper."
    Melo R.G., Leitao A.C., Padula M.
    Yeast 21:991-1003(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  14. "Excision of the oxidatively formed 5-hydroxyhydantoin and 5-hydroxy-5-methylhydantoin pyrimidine lesions by Escherichia coli and Saccharomyces cerevisiae DNA N-glycosylases."
    Gasparutto D., Muller E., Boiteux S., Cadet J.
    Biochim. Biophys. Acta 1790:16-24(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBSTRATES.
  15. "Dynamic compartmentalization of base excision repair proteins in response to nuclear and mitochondrial oxidative stress."
    Griffiths L.M., Swartzlander D., Meadows K.L., Wilkinson K.D., Corbett A.H., Doetsch P.W.
    Mol. Cell. Biol. 29:794-807(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, SUMOYLATION.

Entry informationi

Entry nameiNTH2_YEAST
AccessioniPrimary (citable) accession number: Q08214
Secondary accession number(s): D6W223
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: November 1, 1996
Last modified: July 6, 2016
This is version 136 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 125 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

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.