P09030 (EX3_ECOLI) Reviewed, UniProtKB/Swiss-Prot

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) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

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.
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.

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 response to DNA damage stimulus Inferred from direct assay PubMed 2429316. Source: EcoCyc
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 direct assay PubMed 342234. Source: EcoCyc 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

109

1

By similarity

Active site

151

1

Proton donor/acceptor By similarity

Metal binding

34

1

Magnesium 1 By similarity

Metal binding

151

1

Magnesium 2 By similarity

Metal binding

153

1

Magnesium 2 By similarity

Metal binding

258

1

Magnesium 1 By similarity

Site

153

1

Transition state stabilizer By similarity

Site

229

1

Important for catalytic activity By similarity

Site

259

1

Interaction with DNA substrate By similarity

Experimental info

Sequence conflict

49 – 50

2

KL → NV in AAA24767. Ref.1

Secondary structure

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268

Helix Strand Turn

Details...

Beta strand

2 – 7

6

Helix

11 – 13

3

Helix

15 – 25

11

Beta strand

28 – 33

6

Helix

39 – 41

3

Helix

44 – 49

6

Beta strand

53 – 59

7

Beta strand

62 – 71

10

Beta strand

74 – 80

7

Helix

85 – 88

4

Beta strand

91 – 98

8

Beta strand

101 – 109

9

Helix

121 – 139

19

Beta strand

146 – 151

6

Helix

158 – 160

3

Helix

165 – 174

10

Beta strand

176 – 179

4

Helix

181 – 192

12

Beta strand

195 – 197

3

Helix

198 – 202

5

Turn

215 – 218

4

Helix

219 – 222

4

Beta strand

229 – 234

6

Helix

235 – 238

4

Beta strand

241 – 246

6

Helix

248 – 251

4

Beta strand

253 – 255

3

Beta strand

262 – 266

5

Sequences

	Sequence		Length	Mass (Da)
	P09030 [UniParc]. Last modified November 1, 1997. Version 4. Checksum: 09E0E263DCF38634	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

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] [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. , 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 277:1453-1474(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.

PIR

NCECX3. E64934.

RefSeq

NP_416263.1. NC_000913.2.
YP_490010.1. NC_007779.1.

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.

STRING

511145.b1749.

2D gel databases

SWISS-2DPAGE

P09030.

Proteomic databases

PaxDb

P09030.

PRIDE

P09030.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74819; AAC74819; b1749.
BAA15540; BAA15540; BAA15540.

GeneID

12932910.
946254.

KEGG

ecj:Y75_p1724.
eco:b1749.

PATRIC

32118809. VBIEscCol129921_1822.

Organism-specific databases

EchoBASE

EB1066.

EcoGene

EG11073. xthA.

Phylogenomic databases

eggNOG

COG0708.

HOGENOM

HOG000034587.

KO

K01142.

OMA

EVNAKRW.

ProtClustDB

PRK11756.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P09030.

Family and domain databases

InterPro

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

PANTHER

PTHR22748. PTHR22748. 1 hit.

Pfam

PF03372. Exo_endo_phos. 1 hit.
[Graphical view]

SUPFAM

SSF56219. Exo_endo_phos. 1 hit.

TIGRFAMs

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...

Other

EvolutionaryTrace

P09030.

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:	May 1, 2013
This is version 143 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program