Exodeoxyribonuclease III - Escherichia coli (strain K12)

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P09030 (EX3_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 130. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	268 AA.
Sequence status	Complete.
Protein existence	Evidence 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.
Subunit structure	Monomer.
Sequence similarities	Belongs to the DNA repair enzymes AP/ExoA family.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Ligand	Magnesium Metal-binding
Molecular function	Exonuclease Hydrolase Nuclease
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	intracellular Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro endonuclease activity Inferred from electronic annotation. Source: InterPro exodeoxyribonuclease III activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 268

268

Exodeoxyribonuclease III

PRO_0000200021

Sites

Active site

259

Proton acceptor

Metal binding

Magnesium or manganese

Site

153

Important for substrate recognition

Experimental info

Sequence conflict

49 – 50

KL → NV in AAA24767. Ref.1

Secondary structure

268

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P09030 [UniParc].

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

FASTA

268

30,969

        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' referencesShow '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: 3049539] [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. Horiuchi T. DNA Res. 3:363-377(1996) [PubMed: 9097039] [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 277:1453-1474(1997) [PubMed: 9278503] [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: 16738553] [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: 8948651] [Abstract] Cited for: CHARACTERIZATION.
[7]	"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: 7885481] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
+	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.

PIR

NCECX3. E64934.

RefSeq

NP_416263.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AKO	X-ray	1.70	A	1-268	[»]

ProteinModelPortal

P09030.

SMR

P09030. Positions 1-268.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-11148N.

IntAct

P09030. 16 interactions.

MINT

MINT-1243969.

2D gel databases

SWISS-2DPAGE

P09030.

ECO2DBASE

G028.2. 6TH EDITION.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000001718; EBESCP00000001718; EBESCG00000001415.
EBESCT00000016194; EBESCP00000015485; EBESCG00000015254.

GeneID

946254.

GenomeReviews

Gene locus JW1738 in contig AP009048_GR.
Gene locus b1749 in contig U00096_GR.

KEGG

ecj:JW1738.
eco:b1749.

PATRIC

32118809. VBIEscCol129921_1822.

Organism-specific databases

EchoBASE

EB1066.

EcoGene

EG11073. xthA.

Phylogenomic databases

eggNOG

COG0708.

GeneTree

EBGT00050000009688.

HOGENOM

HBG704164.

OMA

VTIMNGY.

PhylomeDB

P09030.

ProtClustDB

PRK11756.

Enzyme and pathway databases

BioCyc

EcoCyc:EG11073-MONOMER.
MetaCyc:EG11073-MONOMER.

Gene expression databases

Genevestigator

P09030.

Family and domain databases

InterPro

IPR000097. AP_endonuclease_F1.
IPR020847. AP_endonuclease_F1_BS.
IPR020848. AP_endonuclease_F1_CS.
IPR005135. Endo/exonuclease/phosphatase.
IPR004808. ExoDNase_III.
[Graphical view]

K01142.

PANTHER

PTHR22748. ExoIII_xth. 1 hit.

Pfam

PF03372. Exo_endo_phos. 1 hit.
[Graphical view]

SUPFAM

SSF56219. Exo_endo_phos. 1 hit.

TIGRFAMs

TIGR00195. ExoDNase_III. 1 hit.
TIGR00633. Xth. 1 hit.

PROSITE

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]

ProtoNet

Search...

Entry information

Entry name

EX3_ECOLI

Accession

Primary (citable) accession number: P09030

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1988
Last sequence update:	November 1, 1997
Last modified:	January 25, 2012
This is version 130 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Web resources

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents