UniProtKB - P04995 (EX1_ECOLI)
Protein
Exodeoxyribonuclease I
Gene
sbcB
Organism
Escherichia coli (strain K12)
Status
Functioni
Degrades single-stranded DNA (ssDNA) in a highly processive manner (PubMed:23609540). Also functions as a DNA deoxyribophosphodiesterase that releases deoxyribose-phosphate moieties following the cleavage of DNA at an apurinic/apyrimidinic (AP) site by either an AP endonuclease or AP lyase (PubMed:1329027).2 Publications
Catalytic activityi
- Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.3 Publications EC:3.1.11.1
Cofactori
Mg2+4 PublicationsNote: Binds 2 Mg2+ ions per monomer.1 Publication
Activity regulationi
Inhibited by 10 mM EDTA.1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 15 | Magnesium 15 Publications | 1 | |
Metal bindingi | 17 | Magnesium 21 Publication | 1 | |
Binding sitei | 17 | Substrate1 Publication | 1 | |
Sitei | 148 | Important for interaction with ssb1 Publication | 1 | |
Binding sitei | 165 | Substrate1 Publication | 1 | |
Sitei | 181 | Important for activity1 Publication | 1 | |
Metal bindingi | 186 | Magnesium 21 Publication | 1 | |
Sitei | 207 | Important for interaction with ssb1 Publication | 1 | |
Sitei | 311 | Important for interaction with ssb1 Publication | 1 | |
Sitei | 338 | Important for interaction with ssb1 Publication | 1 |
GO - Molecular functioni
- 3'-5'-exoribonuclease activity Source: GO_Central
- 5'-deoxyribose-5-phosphate lyase activity Source: UniProtKB
- exodeoxyribonuclease I activity Source: EcoCyc
- magnesium ion binding Source: UniProtKB
- single-stranded DNA 3'-5' exodeoxyribonuclease activity Source: UniProtKB
- single-stranded DNA binding Source: UniProtKB
GO - Biological processi
- DNA catabolic process Source: EcoCyc
- DNA catabolic process, exonucleolytic Source: UniProtKB
- DNA repair Source: UniProtKB-KW
Keywordsi
Molecular function | DNA-binding, Exonuclease, Hydrolase, Nuclease |
Biological process | DNA damage, DNA repair |
Ligand | Magnesium, Metal-binding, Zinc |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10926-MONOMER MetaCyc:EG10926-MONOMER |
BRENDAi | 3.1.11.1, 2026 |
Names & Taxonomyi
Protein namesi | Recommended name: Exodeoxyribonuclease I (EC:3.1.11.13 Publications)Short name: ExoI1 Publication Short name: Exonuclease I1 Publication Alternative name(s): DNA deoxyribophosphodiesterase Short name: dRPase |
Gene namesi | Name:sbcB Synonyms:cpeA, xonA Ordered Locus Names:b2011, JW1993 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 148 | R → A: Strongly reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 150 | E → A: About 2-fold increased ssb-binding. Weakly increased ssb-independent and ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 181 | H → A: Residual nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 207 | Y → A: Strongly reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 227 | K → A: 7-fold reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 311 | Q → A: 2-fold reduced ssb-binding. Weakly reduced ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 316 | R → A: Strongly reduced ssb-binding. Strongly reduced ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 318 | E → A: About 2-fold increased ssb-binding. No effect on ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 319 | D → A: 2-fold reduced ssb-binding. No effect on ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 327 | R → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 331 | L → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 338 | R → A: 3-fold reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 448 | Q → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 452 | Q → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000087110 | 1 – 475 | Exodeoxyribonuclease IAdd BLAST | 475 |
Proteomic databases
jPOSTi | P04995 |
PaxDbi | P04995 |
PRIDEi | P04995 |
Interactioni
Subunit structurei
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sitei | 18 | Interaction with single-stranded DNA1 Publication | 1 | |
Sitei | 66 | Interaction with single-stranded DNA1 Publication | 1 | |
Sitei | 113 | Interaction with single-stranded DNA1 Publication | 1 | |
Sitei | 124 | Interaction with single-stranded DNA1 Publication | 1 | |
Sitei | 128 | Interaction with single-stranded DNA1 Publication | 1 | |
Sitei | 142 | Interaction with single-stranded DNA1 Publication | 1 | |
Sitei | 164 | Interaction with single-stranded DNACombined sources1 Publication | 1 | |
Sitei | 214 | Interaction with single-stranded DNA1 Publication | 1 | |
Sitei | 257 | Interaction with single-stranded DNACombined sources1 Publication | 1 | |
Sitei | 284 | Interaction with single-stranded DNA1 Publication | 1 | |
Sitei | 304 | Interaction with single-stranded DNACombined sources1 Publication | 1 | |
Sitei | 368 | Interaction with single-stranded DNA1 Publication | 1 | |
Sitei | 371 | Interaction with single-stranded DNA1 Publication | 1 |
Protein-protein interaction databases
BioGRIDi | 4260414, 102 interactors |
DIPi | DIP-10827N |
IntActi | P04995, 7 interactors |
STRINGi | 511145.b2011 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P04995 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P04995 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 13 – 192 | ExonucleaseSequence analysisAdd BLAST | 180 | |
Domaini | 202 – 355 | ExoI SH3-likePROSITE-ProRule annotationAdd BLAST | 154 | |
Domaini | 358 – 475 | ExoI C-terminalPROSITE-ProRule annotationAdd BLAST | 118 |
Domaini
The N-terminal exonuclease domain and the exonuclease C-terminal domain form a central positively charged groove which binds the DNA.2 Publications2 Publications
Phylogenomic databases
eggNOGi | COG2925, Bacteria |
HOGENOMi | CLU_043508_1_1_6 |
InParanoidi | P04995 |
PhylomeDBi | P04995 |
Family and domain databases
Gene3Di | 2.30.30.450, 1 hit 3.30.420.10, 1 hit |
InterProi | View protein in InterPro IPR023607, Exodeoxyribonuclease_I IPR034748, EXOI_C IPR034747, EXOI_SH3 IPR038649, EXOI_SH3_sf IPR013620, Exonuc_1_C IPR013520, Exonuclease_RNaseT/DNA_pol3 IPR012337, RNaseH-like_sf IPR036397, RNaseH_sf |
Pfami | View protein in Pfam PF08411, Exonuc_X-T_C, 1 hit PF00929, RNase_T, 1 hit |
PIRSFi | PIRSF000977, Exodeoxyribonuclease_I, 1 hit |
SMARTi | View protein in SMART SM00479, EXOIII, 1 hit |
SUPFAMi | SSF53098, SSF53098, 1 hit |
PROSITEi | View protein in PROSITE PS51785, EXOI_C, 1 hit PS51784, EXOI_SH3, 1 hit |
i Sequence
Sequence statusi: Complete.
P04995-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MMNDGKQQST FLFHDYETFG THPALDRPAQ FAAIRTDSEF NVIGEPEVFY
60 70 80 90 100
CKPADDYLPQ PGAVLITGIT PQEARAKGEN EAAFAARIHS LFTVPKTCIL
110 120 130 140 150
GYNNVRFDDE VTRNIFYRNF YDPYAWSWQH DNSRWDLLDV MRACYALRPE
160 170 180 190 200
GINWPENDDG LPSFRLEHLT KANGIEHSNA HDAMADVYAT IAMAKLVKTR
210 220 230 240 250
QPRLFDYLFT HRNKHKLMAL IDVPQMKPLV HVSGMFGAWR GNTSWVAPLA
260 270 280 290 300
WHPENRNAVI MVDLAGDISP LLELDSDTLR ERLYTAKTDL GDNAAVPVKL
310 320 330 340 350
VHINKCPVLA QANTLRPEDA DRLGINRQHC LDNLKILREN PQVREKVVAI
360 370 380 390 400
FAEAEPFTPS DNVDAQLYNG FFSDADRAAM KIVLETEPRN LPALDITFVD
410 420 430 440 450
KRIEKLLFNY RARNFPGTLD YAEQQRWLEH RRQVFTPEFL QGYADELQML
460 470
VQQYADDKEK VALLKALWQY AEEIV
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 210 – 218 | Missing in AAA19938 (PubMed:3539937).Curated | 9 | |
Sequence conflicti | 225 | Q → H in AAA19938 (PubMed:3539937).Curated | 1 | |
Sequence conflicti | 343 | V → E in AAA19938 (PubMed:3539937).Curated | 1 | |
Sequence conflicti | 475 | V → A in AAA19938 (PubMed:3539937).Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | J02641 Unassigned DNA Translation: AAA19938.1 U00009 Genomic DNA Translation: AAA16417.1 U00096 Genomic DNA Translation: AAC75072.1 AP009048 Genomic DNA Translation: BAA15839.1 |
PIRi | B64966, NCECX1 |
RefSeqi | NP_416515.1, NC_000913.3 WP_000980589.1, NZ_LN832404.1 |
Genome annotation databases
EnsemblBacteriai | AAC75072; AAC75072; b2011 BAA15839; BAA15839; BAA15839 |
GeneIDi | 946529 |
KEGGi | ecj:JW1993 eco:b2011 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | J02641 Unassigned DNA Translation: AAA19938.1 U00009 Genomic DNA Translation: AAA16417.1 U00096 Genomic DNA Translation: AAC75072.1 AP009048 Genomic DNA Translation: BAA15839.1 |
PIRi | B64966, NCECX1 |
RefSeqi | NP_416515.1, NC_000913.3 WP_000980589.1, NZ_LN832404.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1FXX | X-ray | 2.40 | A | 1-475 | [»] | |
2QXF | X-ray | 1.50 | A | 1-475 | [»] | |
3C94 | X-ray | 2.70 | A | 1-475 | [»] | |
3C95 | X-ray | 1.70 | A | 1-475 | [»] | |
3HL8 | X-ray | 1.55 | A | 1-475 | [»] | |
3HP9 | X-ray | 1.60 | A | 1-475 | [»] | |
4HCB | X-ray | 2.00 | A/B | 1-475 | [»] | |
4HCC | X-ray | 2.96 | A/B | 1-475 | [»] | |
4JRP | X-ray | 1.95 | A/B | 1-475 | [»] | |
4JRQ | X-ray | 3.00 | A/B | 1-475 | [»] | |
4JS4 | X-ray | 3.10 | A/B | 1-475 | [»] | |
4JS5 | X-ray | 3.50 | A/B | 1-475 | [»] | |
SMRi | P04995 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4260414, 102 interactors |
DIPi | DIP-10827N |
IntActi | P04995, 7 interactors |
STRINGi | 511145.b2011 |
Proteomic databases
jPOSTi | P04995 |
PaxDbi | P04995 |
PRIDEi | P04995 |
Genome annotation databases
EnsemblBacteriai | AAC75072; AAC75072; b2011 BAA15839; BAA15839; BAA15839 |
GeneIDi | 946529 |
KEGGi | ecj:JW1993 eco:b2011 |
Organism-specific databases
EchoBASEi | EB0919 |
Phylogenomic databases
eggNOGi | COG2925, Bacteria |
HOGENOMi | CLU_043508_1_1_6 |
InParanoidi | P04995 |
PhylomeDBi | P04995 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10926-MONOMER MetaCyc:EG10926-MONOMER |
BRENDAi | 3.1.11.1, 2026 |
Miscellaneous databases
EvolutionaryTracei | P04995 |
PROi | PR:P04995 |
Family and domain databases
Gene3Di | 2.30.30.450, 1 hit 3.30.420.10, 1 hit |
InterProi | View protein in InterPro IPR023607, Exodeoxyribonuclease_I IPR034748, EXOI_C IPR034747, EXOI_SH3 IPR038649, EXOI_SH3_sf IPR013620, Exonuc_1_C IPR013520, Exonuclease_RNaseT/DNA_pol3 IPR012337, RNaseH-like_sf IPR036397, RNaseH_sf |
Pfami | View protein in Pfam PF08411, Exonuc_X-T_C, 1 hit PF00929, RNase_T, 1 hit |
PIRSFi | PIRSF000977, Exodeoxyribonuclease_I, 1 hit |
SMARTi | View protein in SMART SM00479, EXOIII, 1 hit |
SUPFAMi | SSF53098, SSF53098, 1 hit |
PROSITEi | View protein in PROSITE PS51785, EXOI_C, 1 hit PS51784, EXOI_SH3, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | EX1_ECOLI | |
Accessioni | P04995Primary (citable) accession number: P04995 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | August 13, 1987 |
Last sequence update: | February 1, 1994 | |
Last modified: | April 7, 2021 | |
This is version 185 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references