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P09030 (EX3_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 149. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Exodeoxyribonuclease III

Short name=EXO III
Short name=Exonuclease III
EC=3.1.11.2
Alternative name(s):
AP endonuclease VI
Gene names
Name:xthA
Synonyms:xth
Ordered Locus Names:b1749, JW1738
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length268 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 activity

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

Cofactor

Magnesium. Can also utilize manganese. Probably binds two magnesium or manganese ions per subunit By similarity. Ref.8

Subunit structure

Monomer.

Sequence similarities

Belongs to the DNA repair enzymes AP/ExoA family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 268268Exodeoxyribonuclease III
PRO_0000200021

Sites

Active site1091 By similarity
Active site1511Proton donor/acceptor By similarity
Metal binding341Magnesium 1 By similarity
Metal binding1511Magnesium 2 By similarity
Metal binding1531Magnesium 2 By similarity
Metal binding2581Magnesium 1 By similarity
Site1531Transition state stabilizer By similarity
Site2291Important for catalytic activity By similarity
Site2591Interaction with DNA substrate By similarity

Experimental info

Sequence conflict49 – 502KL → NV in AAA24767. Ref.1

Secondary structure

...................................................... 268
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P09030 [UniParc].

Last modified November 1, 1997. Version 4.
Checksum: 09E0E263DCF38634

FASTA26830,969
        10         20         30         40         50         60 
MKFVSFNING LRARPHQLEA IVEKHQPDVI GLQETKVHDD MFPLEEVAKL GYNVFYHGQK 

        70         80         90        100        110        120 
GHYGVALLTK ETPIAVRRGF PGDDEEAQRR IIMAEIPSLL GNVTVINGYF PQGESRDHPI 

       130        140        150        160        170        180 
KFPAKAQFYQ NLQNYLETEL KRDNPVLIMG DMNISPTDLD IGIGEENRKR WLRTGKCSFL 

       190        200        210        220        230        240 
PEEREWMDRL MSWGLVDTFR HANPQTADRF SWFDYRSKGF DDNRGLRIDL LLASQPLAEC 

       250        260 
CVETGIDYEI RSMEKPSDHA PVWATFRR 

« Hide

References

« Hide 'large scale' references
[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]"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map."
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. expand/collapse author list , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Web resources

Wikipedia

Exonuclease III entry

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X13002 Genomic DNA. Translation: CAA31424.1.
M22592 Genomic DNA. Translation: AAA24767.1.
U00096 Genomic DNA. Translation: AAC74819.1.
AP009048 Genomic DNA. Translation: BAA15540.1.
PIRNCECX3. E64934.
RefSeqNP_416263.1. NC_000913.3.
YP_490010.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1AKOX-ray1.70A1-268[»]
ProteinModelPortalP09030.
SMRP09030. Positions 1-268.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-11148N.
IntActP09030. 16 interactions.
MINTMINT-1243969.
STRING511145.b1749.

2D gel databases

SWISS-2DPAGEP09030.

Proteomic databases

PaxDbP09030.
PRIDEP09030.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74819; AAC74819; b1749.
BAA15540; BAA15540; BAA15540.
GeneID12932910.
946254.
KEGGecj:Y75_p1724.
eco:b1749.
PATRIC32118809. VBIEscCol129921_1822.

Organism-specific databases

EchoBASEEB1066.
EcoGeneEG11073. xthA.

Phylogenomic databases

eggNOGCOG0708.
HOGENOMHOG000034587.
KOK01142.
OMAHETKFPA.
OrthoDBEOG60SCPF.
PhylomeDBP09030.
ProtClustDBPRK11756.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP09030.

Family and domain databases

Gene3D3.60.10.10. 1 hit.
InterProIPR004808. AP_endonuc_1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
[Graphical view]
PANTHERPTHR22748. PTHR22748. 1 hit.
PfamPF03372. Exo_endo_phos. 1 hit.
[Graphical view]
SUPFAMSSF56219. SSF56219. 1 hit.
TIGRFAMsTIGR00633. xth. 1 hit.
PROSITEPS00726. 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]
ProtoNetSearch...

Other

EvolutionaryTraceP09030.
PROP09030.

Entry information

Entry nameEX3_ECOLI
AccessionPrimary (citable) accession number: P09030
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: November 1, 1997
Last modified: April 16, 2014
This is version 149 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene