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Endonuclease III (EC 4.2.99.18) (DNA-(apurinic or apyrimidinic site) lyase)
F4ATR5_GLAS4 Unreviewed; 210 AA.
F4ATR5;
28-JUN-2011, integrated into UniProtKB/TrEMBL.
28-JUN-2011, sequence version 1.
28-FEB-2018, entry version 47.
RecName: Full=Endonuclease III {ECO:0000256|HAMAP-Rule:MF_00942};
EC=4.2.99.18 {ECO:0000256|HAMAP-Rule:MF_00942};
AltName: Full=DNA-(apurinic or apyrimidinic site) lyase {ECO:0000256|HAMAP-Rule:MF_00942};
Name=nth {ECO:0000256|HAMAP-Rule:MF_00942};
OrderedLocusNames=Glaag_1354 {ECO:0000313|EMBL:AEE22314.1};
Glaciecola sp. (strain 4H-3-7+YE-5).
Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
Alteromonadaceae; Glaciecola.
NCBI_TaxID=983545 {ECO:0000313|EMBL:AEE22314.1, ECO:0000313|Proteomes:UP000006544};
[1] {ECO:0000313|EMBL:AEE22314.1, ECO:0000313|Proteomes:UP000006544}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=4H-3-7+YE-5 {ECO:0000313|EMBL:AEE22314.1,
ECO:0000313|Proteomes:UP000006544};
PubMed=21705587; DOI=10.1128/JB.05468-11;
US DOE Joint Genome Institute;
Klippel B., Lochner A., Bruce D.C., Davenport K.W., Detter C.,
Goodwin L.A., Han J., Han S., Land M.L., Mikhailova N., Nolan M.,
Pennacchio L., Pitluck S., Tapia R., Woyke T., Wiebusch S., Basner A.,
Abe F., Horikoshi K., Keller M., Antranikian G.;
"Complete genome sequence of the marine, cellulose and xylan degrading
bacterium Glaciecola sp. 4H-3-7+YE-5.";
J. Bacteriol. 193:4547-4548(2011).
[2]
NUCLEOTIDE SEQUENCE.
STRAIN=4H-3-7+YE-5;
US DOE Joint Genome Institute;
Lucas S., Copeland A., Lapidus A., Cheng J.-F., Goodwin L.,
Pitluck S., Davenport K., Detter J.C., Han C., Tapia R., Land M.,
Hauser L., Kyrpides N., Ivanova N., Mikhailova N., Pagani I.,
Piela B., Lochner A., Antranikian F.I., Woyke T.;
"Complete sequence of chromosome of Glaciecola sp. 4H-3-7+YE-5.";
Submitted (FEB-2011) to the EMBL/GenBank/DDBJ databases.
-!- FUNCTION: 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.
{ECO:0000256|HAMAP-Rule:MF_00942}.
-!- CATALYTIC ACTIVITY: 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. {ECO:0000256|HAMAP-Rule:MF_00942}.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000256|HAMAP-Rule:MF_00942};
Note=Binds 1 [4Fe-4S] cluster. {ECO:0000256|HAMAP-Rule:MF_00942};
-!- SIMILARITY: Belongs to the Nth/MutY family. {ECO:0000256|HAMAP-
Rule:MF_00942}.
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EMBL; CP002526; AEE22314.1; -; Genomic_DNA.
RefSeq; WP_013753254.1; NC_015497.1.
STRING; 983545.Glaag_1354; -.
EnsemblBacteria; AEE22314; AEE22314; Glaag_1354.
KEGG; gag:Glaag_1354; -.
eggNOG; ENOG4105CSM; Bacteria.
eggNOG; COG0177; LUCA.
KO; K10773; -.
OrthoDB; POG091H021U; -.
BioCyc; GSP983545:G1GX6-1402-MONOMER; -.
Proteomes; UP000006544; Chromosome.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) lyase activity; IEA:UniProtKB-EC.
GO; GO:0140080; F:class III/IV DNA-(apurinic or apyrimidinic site) lyase activity; IEA:UniProtKB-EC.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
GO; GO:0019104; F:DNA N-glycosylase activity; IEA:UniProtKB-UniRule.
GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0006284; P:base-excision repair; IEA:InterPro.
CDD; cd00056; ENDO3c; 1.
Gene3D; 1.10.1670.10; -; 2.
HAMAP; MF_00942; Nth; 1.
InterPro; IPR011257; DNA_glycosylase.
InterPro; IPR004036; Endonuclease-III-like_CS2.
InterPro; IPR003651; Endonuclease3_FeS-loop_motif.
InterPro; IPR004035; Endouclease-III_FeS-bd_BS.
InterPro; IPR003265; HhH-GPD_domain.
InterPro; IPR000445; HhH_motif.
InterPro; IPR023170; HTH_base_excis_C.
InterPro; IPR005759; Nth.
Pfam; PF10576; EndIII_4Fe-2S; 1.
Pfam; PF00633; HHH; 1.
Pfam; PF00730; HhH-GPD; 1.
SMART; SM00478; ENDO3c; 1.
SMART; SM00525; FES; 1.
SUPFAM; SSF48150; SSF48150; 1.
TIGRFAMs; TIGR01083; nth; 1.
PROSITE; PS00764; ENDONUCLEASE_III_1; 1.
PROSITE; PS01155; ENDONUCLEASE_III_2; 1.
3: Inferred from homology;
4Fe-4S {ECO:0000256|HAMAP-Rule:MF_00942};
Complete proteome {ECO:0000313|Proteomes:UP000006544};
DNA damage {ECO:0000256|HAMAP-Rule:MF_00942};
DNA repair {ECO:0000256|HAMAP-Rule:MF_00942};
DNA-binding {ECO:0000256|HAMAP-Rule:MF_00942};
Endonuclease {ECO:0000313|EMBL:AEE22314.1};
Glycosidase {ECO:0000256|HAMAP-Rule:MF_00942};
Hydrolase {ECO:0000256|HAMAP-Rule:MF_00942,
ECO:0000313|EMBL:AEE22314.1}; Iron {ECO:0000256|HAMAP-Rule:MF_00942};
Iron-sulfur {ECO:0000256|HAMAP-Rule:MF_00942};
Lyase {ECO:0000256|HAMAP-Rule:MF_00942, ECO:0000313|EMBL:AEE22314.1};
Metal-binding {ECO:0000256|HAMAP-Rule:MF_00942};
Nuclease {ECO:0000313|EMBL:AEE22314.1}.
DOMAIN 38 185 ENDO3c. {ECO:0000259|SMART:SM00478}.
METAL 187 187 Iron-sulfur (4Fe-4S). {ECO:0000256|HAMAP-
Rule:MF_00942}.
METAL 194 194 Iron-sulfur (4Fe-4S). {ECO:0000256|HAMAP-
Rule:MF_00942}.
METAL 197 197 Iron-sulfur (4Fe-4S). {ECO:0000256|HAMAP-
Rule:MF_00942}.
METAL 203 203 Iron-sulfur (4Fe-4S). {ECO:0000256|HAMAP-
Rule:MF_00942}.
SEQUENCE 210 AA; 23474 MW; 5175E0FEA12F29C7 CRC64;
MNQQKRIEML TRWRAANPHP TTELNFTSPF ELLIAVLLSA QATDVSVNKA MAKMFPVANT
PETVYALGVD GVKEFIKTIG LFNTKAVNVN KTCKMLIDKH NSVVPEDRAA LEALPGVGRK
TANVVLNTAF GWPTIAVDTH IDRVSNRTKF AMGKTVEKVE EKLLKVVPAE FKVDVHHWLI
LHGRYTCIAR KPRCGSCIIE DLCEFKDKTE
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Pathways :
WP1030: Selenium metabolism Selenoproteins
WP108: Selenium metabolism/Selenoproteins
WP1149: Selenium metabolism Selenoproteins
WP1293: Selenium metabolism Selenoproteins
WP1358: Selenium metabolism Selenoproteins
WP1640: Cysteine and methionine metabolism
WP1700: Selenoamino acid metabolism
WP1705: Sulfur metabolism
WP1718: Vitamin B6 metabolism
WP28: Selenium Metabolism and Selenoproteins
WP390: Serine-isocitrate lyase pathway
WP668: Octadecanoid Pathway
Related Genes :
[AI4 ENS2 I-SCEII Q0065] Intron-encoded DNA endonuclease aI4 (DNA endonuclease I-SceII) [Cleaved into: Truncated non-functional cytochrome oxidase 1; DNA endonuclease aI4 (EC 3.1.-.-) (Intron-encoded endonuclease I-SceII)]
[AI3 ENS3 I-SCEIII Q0060] Intron-encoded DNA endonuclease aI3 (DNA endonuclease I-SceIII) [Cleaved into: Truncated non-functional cytochrome oxidase 1; DNA endonuclease aI3 (EC 3.1.-.-) (Intron-encoded endonuclease I-SceIII)]
[AI5_ALPHA I-SCEIV Q0070] Intron-encoded DNA endonuclease aI5 alpha (DNA endonuclease I-SceIV) [Cleaved into: Truncated non-functional cytochrome oxidase 1; DNA endonuclease aI5 alpha (EC 3.1.-.-) (Intron-encoded endonuclease I-SceIV)]
[RAD27 FEN1 RTH1 YKL113C YKL510] Flap endonuclease 1 (FEN-1) (EC 3.1.-.-) (Flap structure-specific endonuclease 1) (RAD2 homolog nuclease 1) (RTH1 nuclease) (Structure-specific endonuclease RAD27)
[SEN2 YLR105C L8004.12] tRNA-splicing endonuclease subunit SEN2 (EC 4.6.1.16) (Splicing endonuclease protein 2) (tRNA-intron endonuclease SEN2)
[Gen CG10670] Flap endonuclease GEN (EC 3.1.-.-) (Flap structure-specific endonuclease GEN) (Xpg-like endonuclease) (DmGEN)
[APEX2 APE2 APEXL2 XTH2] DNA-(apurinic or apyrimidinic site) lyase 2 (EC 3.1.-.-) (EC 4.2.99.18) (AP endonuclease XTH2) (APEX nuclease 2) (APEX nuclease-like 2) (Apurinic-apyrimidinic endonuclease 2) (AP endonuclease 2)
[FEN1 RAD2] Flap endonuclease 1 (FEN-1) (EC 3.1.-.-) (DNase IV) (Flap structure-specific endonuclease 1) (Maturation factor 1) (MF1) (hFEN-1)
[APEX1 APE APE1 APEX APX HAP1 REF1] DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-) (EC 4.2.99.18) (APEX nuclease) (APEN) (Apurinic-apyrimidinic endonuclease 1) (AP endonuclease 1) (APE-1) (REF-1) (Redox factor-1) [Cleaved into: DNA-(apurinic or apyrimidinic site) lyase, mitochondrial]
[cas3 TTHB187] CRISPR-associated endonuclease/helicase Cas3 (EC 3.1.-.-) (EC 3.6.4.-) (CRISPR-associated ssDNA endonuclease/helicase Cas3)
[TSEN15 C1orf19 SEN15] tRNA-splicing endonuclease subunit Sen15 (SEN15 homolog) (HsSEN15) (tRNA-intron endonuclease Sen15)
[VMA1 CLS8 TFP1 YDL185W D1286] V-type proton ATPase catalytic subunit A (V-ATPase subunit A) (EC 3.6.3.14) (Vacuolar proton pump subunit A) [Cleaved into: Endonuclease PI-SceI (EC 3.1.-.-) (Sce VMA intein) (VMA1-derived endonuclease) (VDE)]
[cas12a cpf1 FTN_1397] CRISPR-associated endonuclease Cas12a (EC 3.1.21.1) (EC 3.1.27.2) (CRISPR-associated endonuclease Cpf1) (FnCas12a) (FnCpf1)
[ZRANB3] DNA annealing helicase and endonuclease ZRANB3 (Annealing helicase 2) (AH2) (Zinc finger Ran-binding domain-containing protein 3) [Includes: DNA annealing helicase ZRANB3 (EC 3.6.4.-); Endonuclease ZRANB3 (EC 3.1.-.-)]
[TSEN34 LENG5 SEN34] tRNA-splicing endonuclease subunit Sen34 (EC 4.6.1.16) (Leukocyte receptor cluster member 5) (tRNA-intron endonuclease Sen34) (HsSen34)
[TSEN2 SEN2] tRNA-splicing endonuclease subunit Sen2 (EC 4.6.1.16) (tRNA-intron endonuclease Sen2) (HsSen2)
[NTG1 OGG2 SCR1 YAL015C FUN33] Endonuclease III homolog 1 (EC 3.2.2.-) (EC 4.2.99.18) (Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase 1) (DNA glycosylase/AP lyase 1) (Endonuclease III-like glycosylase 1) (Redoxyendonuclease 1)
[nei b0714 JW0704] Endonuclease 8 (DNA glycosylase/AP lyase Nei) (EC 3.2.2.-) (EC 4.2.99.18) (DNA-(apurinic or apyrimidinic site) lyase Nei) (Endonuclease VIII)
[TSEN54 SEN54] tRNA-splicing endonuclease subunit Sen54 (SEN54 homolog) (HsSEN54) (tRNA-intron endonuclease Sen54)
[NTG2 SCR2 YOL043C] Endonuclease III homolog 2 (EC 3.2.2.-) (EC 4.2.99.18) (Bifunctional DNA N-glycosylase/DNA-(apurinic or apyrimidinic site) lyase 2) (DNA glycosylase/AP lyase 2) (Endonuclease III-like glycosylase 2) (Redoxyendonuclease 2)
[cas12b c2c1 N007_06525] CRISPR-associated endonuclease Cas12b (EC 3.1.-.-) (AacC2c1) (CRISPR-associated endonuclease C2c1)
[FEN1A Os05g0540100 LOC_Os05g46270 OsJ_19381 OSJNBa0052K01.23] Flap endonuclease 1-A (FEN-1-A) (EC 3.1.-.-) (Flap structure-specific endonuclease 1-A) (OsFEN-1) (OsFEN-1a)
[Fen1 Fen-1] Flap endonuclease 1 (FEN-1) (EC 3.1.-.-) (Flap structure-specific endonuclease 1)
[Fen1] Flap endonuclease 1 (FEN-1) (EC 3.1.-.-) (Flap structure-specific endonuclease 1)
[cas12a cpf1 HMPREF1246_0236] CRISPR-associated endonuclease Cas12a (EC 3.1.21.1) (EC 3.1.27.2) (AsCpf1) (CRISPR-associated endonuclease Cpf1)
[Apex1 Ape Apex Ref1] DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-) (EC 4.2.99.18) (APEX nuclease) (APEN) (Apurinic-apyrimidinic endonuclease 1) (AP endonuclease 1) (REF-1) (Redox factor-1) [Cleaved into: DNA-(apurinic or apyrimidinic site) lyase, mitochondrial]
[Apex1 Ape Apex Ref1] DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-) (EC 4.2.99.18) (APEX nuclease) (APEN) (Apurinic-apyrimidinic endonuclease 1) (AP endonuclease 1) (REF-1) (Redox factor-1) [Cleaved into: DNA-(apurinic or apyrimidinic site) lyase, mitochondrial]
[APEX1 APE APEX BAP1 REF1] DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-) (EC 4.2.99.18) (APEX nuclease) (APEN) (Apurinic-apyrimidinic endonuclease 1) (AP endonuclease 1) (REF-1) (Redox factor-1) [Cleaved into: DNA-(apurinic or apyrimidinic site) lyase, mitochondrial]
[apn2 SPBC3D6.10] DNA-(apurinic or apyrimidinic site) lyase 2 (EC 4.2.99.18) (AP endonuclease 2) (Apurinic-apyrimidinic endonuclease 2)
[apex1 apex1a apex1b si:ch211-214j24.12 zgc:66204] DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.-.-) (EC 4.2.99.18) (APEX nuclease) (APEN) (Apurinic-apyrimidinic endonuclease 1) (AP endonuclease 1) (zAP1)
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