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Protein

Exodeoxyribonuclease III

Gene

xthA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

Mg2+By similarity, Mn2+By similarityNote: Probably binds two magnesium or manganese ions per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi34Magnesium 1By similarity1
Active sitei109By similarity1
Active sitei151Proton donor/acceptorBy similarity1
Metal bindingi151Magnesium 2By similarity1
Metal bindingi153Magnesium 2By similarity1
Sitei153Transition state stabilizerBy similarity1
Sitei229Important for catalytic activityBy similarity1
Metal bindingi258Magnesium 1By similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease
Biological processDNA damage, DNA repair
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11073-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11073 xthA

Subcellular locationi

GO - Cellular componenti

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002000211 – 268Exodeoxyribonuclease IIIAdd BLAST268

Proteomic databases

PaxDbiP09030
PRIDEiP09030

2D gel databases

SWISS-2DPAGEiP09030

Interactioni

Subunit structurei

Monomer.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei259Interaction with DNA substrateBy similarity1

Protein-protein interaction databases

BioGridi4261904, 84 interactors
DIPiDIP-11148N
IntActiP09030, 17 interactors
STRINGi316385.ECDH10B_1887

Structurei

Secondary structure

1268
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP09030
SMRiP09030
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP09030

Family & Domainsi

Sequence similaritiesi

Belongs to the DNA repair enzymes AP/ExoA family.Curated

Phylogenomic databases

eggNOGiENOG4105CGK Bacteria
COG0708 LUCA
HOGENOMiHOG000034587
InParanoidiP09030
KOiK01142
PhylomeDBiP09030

Family and domain databases

CDDicd09086 ExoIII-like_AP-endo, 1 hit
Gene3Di3.60.10.10, 1 hit
InterProiView protein in InterPro
IPR004808 AP_endonuc_1
IPR020847 AP_endonuclease_F1_BS
IPR020848 AP_endonuclease_F1_CS
IPR036691 Endo/exonu/phosph_ase_sf
IPR005135 Endo/exonuclease/phosphatase
IPR037493 ExoIII-like
PANTHERiPTHR43250 PTHR43250, 1 hit
PfamiView protein in Pfam
PF03372 Exo_endo_phos, 1 hit
SUPFAMiSSF56219 SSF56219, 1 hit
TIGRFAMsiTIGR00633 xth, 1 hit
PROSITEiView protein in 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

Sequencei

Sequence statusi: Complete.

P09030-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKFVSFNING LRARPHQLEA IVEKHQPDVI GLQETKVHDD MFPLEEVAKL
60 70 80 90 100
GYNVFYHGQK GHYGVALLTK ETPIAVRRGF PGDDEEAQRR IIMAEIPSLL
110 120 130 140 150
GNVTVINGYF PQGESRDHPI KFPAKAQFYQ NLQNYLETEL KRDNPVLIMG
160 170 180 190 200
DMNISPTDLD IGIGEENRKR WLRTGKCSFL PEEREWMDRL MSWGLVDTFR
210 220 230 240 250
HANPQTADRF SWFDYRSKGF DDNRGLRIDL LLASQPLAEC CVETGIDYEI
260
RSMEKPSDHA PVWATFRR
Length:268
Mass (Da):30,969
Last modified:November 1, 1997 - v4
Checksum:i09E0E263DCF38634
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti49 – 50KL → NV in AAA24767 (PubMed:3049539).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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
WP_000673918.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC74819; AAC74819; b1749
BAA15540; BAA15540; BAA15540
GeneIDi946254
KEGGiecj:JW1738
eco:b1749
PATRICifig|1411691.4.peg.506

Similar proteinsi

Cross-referencesi

Web resourcesi

Wikipedia

Exonuclease III entry

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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
WP_000673918.1, NZ_LN832404.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1AKOX-ray1.70A1-268[»]
ProteinModelPortaliP09030
SMRiP09030
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261904, 84 interactors
DIPiDIP-11148N
IntActiP09030, 17 interactors
STRINGi316385.ECDH10B_1887

2D gel databases

SWISS-2DPAGEiP09030

Proteomic databases

PaxDbiP09030
PRIDEiP09030

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74819; AAC74819; b1749
BAA15540; BAA15540; BAA15540
GeneIDi946254
KEGGiecj:JW1738
eco:b1749
PATRICifig|1411691.4.peg.506

Organism-specific databases

EchoBASEiEB1066
EcoGeneiEG11073 xthA

Phylogenomic databases

eggNOGiENOG4105CGK Bacteria
COG0708 LUCA
HOGENOMiHOG000034587
InParanoidiP09030
KOiK01142
PhylomeDBiP09030

Enzyme and pathway databases

BioCyciEcoCyc:EG11073-MONOMER
MetaCyc:EG11073-MONOMER

Miscellaneous databases

EvolutionaryTraceiP09030
PROiPR:P09030

Family and domain databases

CDDicd09086 ExoIII-like_AP-endo, 1 hit
Gene3Di3.60.10.10, 1 hit
InterProiView protein in InterPro
IPR004808 AP_endonuc_1
IPR020847 AP_endonuclease_F1_BS
IPR020848 AP_endonuclease_F1_CS
IPR036691 Endo/exonu/phosph_ase_sf
IPR005135 Endo/exonuclease/phosphatase
IPR037493 ExoIII-like
PANTHERiPTHR43250 PTHR43250, 1 hit
PfamiView protein in Pfam
PF03372 Exo_endo_phos, 1 hit
SUPFAMiSSF56219 SSF56219, 1 hit
TIGRFAMsiTIGR00633 xth, 1 hit
PROSITEiView protein in 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
ProtoNetiSearch...

Entry informationi

Entry nameiEX3_ECOLI
AccessioniPrimary (citable) accession number: P09030
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: November 1, 1997
Last modified: November 7, 2018
This is version 183 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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