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P09030

- EX3_ECOLI

UniProt

P09030 - EX3_ECOLI

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Protein
Exodeoxyribonuclease III
Gene
xthA, xth, b1749, JW1738
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Major apurinic-apyrimidinic endonuclease of E.coli. It removes the damaged DNA at cytosines and guanines by cleaving on the 3'-side of the AP site by a beta-elimination reaction. It exhibits 3'-5'-exonuclease, 3'-phosphomonoesterase, 3'-repair diesterase and ribonuclease H activities.

Catalytic activityi

Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.

Cofactori

Magnesium. Can also utilize manganese. Probably binds two magnesium or manganese ions per subunit By similarity.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi34 – 341Magnesium 1 By similarity
Active sitei109 – 1091 By similarity
Active sitei151 – 1511Proton donor/acceptor By similarity
Metal bindingi151 – 1511Magnesium 2 By similarity
Metal bindingi153 – 1531Magnesium 2 By similarity
Sitei153 – 1531Transition state stabilizer By similarity
Sitei229 – 2291Important for catalytic activity By similarity
Metal bindingi258 – 2581Magnesium 1 By similarity
Sitei259 – 2591Interaction with DNA substrate By similarity

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. DNA-(apurinic or apyrimidinic site) lyase activity Source: RefGenome
  3. double-stranded DNA 3'-5' exodeoxyribonuclease activity Source: RefGenome
  4. exodeoxyribonuclease III activity Source: EcoCyc
  5. exonuclease activity Source: EcoCyc
  6. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. DNA catabolic process, endonucleolytic Source: GOC
  2. DNA catabolic process, exonucleolytic Source: GOC
  3. base-excision repair Source: RefGenome
  4. cellular response to DNA damage stimulus Source: EcoCyc
  5. nucleic acid phosphodiester bond hydrolysis Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11073-MONOMER.
ECOL316407:JW1738-MONOMER.
MetaCyc:EG11073-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Exodeoxyribonuclease III (EC:3.1.11.2)
Short name:
EXO III
Short name:
Exonuclease III
Alternative name(s):
AP endonuclease VI
Gene namesi
Name:xthA
Synonyms:xth
Ordered Locus Names:b1749, JW1738
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG11073. xthA.

Subcellular locationi

GO - Cellular componenti

  1. intracellular Source: InterPro
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 268268Exodeoxyribonuclease III
PRO_0000200021Add
BLAST

Proteomic databases

PaxDbiP09030.
PRIDEiP09030.

2D gel databases

SWISS-2DPAGEP09030.

Expressioni

Gene expression databases

GenevestigatoriP09030.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

DIPiDIP-11148N.
IntActiP09030. 16 interactions.
MINTiMINT-1243969.
STRINGi511145.b1749.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 76
Helixi11 – 133
Helixi15 – 2511
Beta strandi28 – 336
Helixi39 – 413
Helixi44 – 496
Beta strandi53 – 597
Beta strandi62 – 7110
Beta strandi74 – 807
Helixi85 – 884
Beta strandi91 – 988
Beta strandi101 – 1099
Helixi121 – 13919
Beta strandi146 – 1516
Helixi158 – 1603
Helixi165 – 17410
Beta strandi176 – 1794
Helixi181 – 19212
Beta strandi195 – 1973
Helixi198 – 2025
Turni215 – 2184
Helixi219 – 2224
Beta strandi229 – 2346
Helixi235 – 2384
Beta strandi241 – 2466
Helixi248 – 2514
Beta strandi253 – 2553
Beta strandi262 – 2665

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AKOX-ray1.70A1-268[»]
ProteinModelPortaliP09030.

Miscellaneous databases

EvolutionaryTraceiP09030.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0708.
HOGENOMiHOG000034587.
KOiK01142.
OMAiIEKPSDH.
OrthoDBiEOG60SCPF.
PhylomeDBiP09030.

Family and domain databases

Gene3Di3.60.10.10. 1 hit.
InterProiIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PANTHERiPTHR22748. PTHR22748. 1 hit.
PfamiPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
SUPFAMiSSF56219. SSF56219. 1 hit.
TIGRFAMsiTIGR00633. xth. 1 hit.
PROSITEiPS00726. AP_NUCLEASE_F1_1. 1 hit.
PS00727. AP_NUCLEASE_F1_2. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P09030-1 [UniParc]FASTAAdd to Basket

« Hide

MKFVSFNING LRARPHQLEA IVEKHQPDVI GLQETKVHDD MFPLEEVAKL    50
GYNVFYHGQK GHYGVALLTK ETPIAVRRGF PGDDEEAQRR IIMAEIPSLL 100
GNVTVINGYF PQGESRDHPI KFPAKAQFYQ NLQNYLETEL KRDNPVLIMG 150
DMNISPTDLD IGIGEENRKR WLRTGKCSFL PEEREWMDRL MSWGLVDTFR 200
HANPQTADRF SWFDYRSKGF DDNRGLRIDL LLASQPLAEC CVETGIDYEI 250
RSMEKPSDHA PVWATFRR 268
Length:268
Mass (Da):30,969
Last modified:November 1, 1997 - v4
Checksum:i09E0E263DCF38634
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti49 – 502KL → NV in AAA24767. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X13002 Genomic DNA. Translation: CAA31424.1.
M22592 Genomic DNA. Translation: AAA24767.1.
U00096 Genomic DNA. Translation: AAC74819.1.
AP009048 Genomic DNA. Translation: BAA15540.1.
PIRiE64934. NCECX3.
RefSeqiNP_416263.1. NC_000913.3.
YP_490010.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC74819; AAC74819; b1749.
BAA15540; BAA15540; BAA15540.
GeneIDi12932910.
946254.
KEGGiecj:Y75_p1724.
eco:b1749.
PATRICi32118809. VBIEscCol129921_1822.

Cross-referencesi

Web resourcesi

Wikipedia

Exonuclease III entry

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X13002 Genomic DNA. Translation: CAA31424.1 .
M22592 Genomic DNA. Translation: AAA24767.1 .
U00096 Genomic DNA. Translation: AAC74819.1 .
AP009048 Genomic DNA. Translation: BAA15540.1 .
PIRi E64934. NCECX3.
RefSeqi NP_416263.1. NC_000913.3.
YP_490010.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AKO X-ray 1.70 A 1-268 [» ]
ProteinModelPortali P09030.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-11148N.
IntActi P09030. 16 interactions.
MINTi MINT-1243969.
STRINGi 511145.b1749.

2D gel databases

SWISS-2DPAGE P09030.

Proteomic databases

PaxDbi P09030.
PRIDEi P09030.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC74819 ; AAC74819 ; b1749 .
BAA15540 ; BAA15540 ; BAA15540 .
GeneIDi 12932910.
946254.
KEGGi ecj:Y75_p1724.
eco:b1749.
PATRICi 32118809. VBIEscCol129921_1822.

Organism-specific databases

EchoBASEi EB1066.
EcoGenei EG11073. xthA.

Phylogenomic databases

eggNOGi COG0708.
HOGENOMi HOG000034587.
KOi K01142.
OMAi IEKPSDH.
OrthoDBi EOG60SCPF.
PhylomeDBi P09030.

Enzyme and pathway databases

BioCyci EcoCyc:EG11073-MONOMER.
ECOL316407:JW1738-MONOMER.
MetaCyc:EG11073-MONOMER.

Miscellaneous databases

EvolutionaryTracei P09030.
PROi P09030.

Gene expression databases

Genevestigatori P09030.

Family and domain databases

Gene3Di 3.60.10.10. 1 hit.
InterProi IPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view ]
PANTHERi PTHR22748. PTHR22748. 1 hit.
Pfami PF03372. Exo_endo_phos. 1 hit.
[Graphical view ]
SUPFAMi SSF56219. SSF56219. 1 hit.
TIGRFAMsi TIGR00633. xth. 1 hit.
PROSITEi PS00726. AP_NUCLEASE_F1_1. 1 hit.
PS00727. AP_NUCLEASE_F1_2. 1 hit.
PS00728. AP_NUCLEASE_F1_3. 1 hit.
PS51435. AP_NUCLEASE_F1_4. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the xth gene of Escherichia coli K-12."
    Saporito S.M., Smith-White B.J., Cunningham R.P.
    J. Bacteriol. 170:4542-4547(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Wurst H., Hoheisel J.D., Pohl F.M.
    Submitted (NOV-1988) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "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.
  6. "Cleavage of single- and double-stranded DNAs containing an abasic residue by Escherichia coli exonuclease III (AP endonuclease VI)."
    Shida T., Noda M., Sekiguchi J.
    Nucleic Acids Res. 24:4572-4576(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  7. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  8. "Structure and function of the multifunctional DNA-repair enzyme exonuclease III."
    Mol C.D., Kuo C.-F., Thayer M.M., Cunningham R.P., Tainer J.A.
    Nature 374:381-386(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), COFACTOR.

Entry informationi

Entry nameiEX3_ECOLI
AccessioniPrimary (citable) accession number: P09030
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: November 1, 1997
Last modified: September 3, 2014
This is version 153 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, 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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