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Protein

Exodeoxyribonuclease I

Gene

sbcB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

Cofactori

Mg2+4 PublicationsNote: Binds 2 Mg2+ ions per monomer.1 Publication

Enzyme regulationi

Inhibited by 10 mM EDTA.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi15Magnesium 15 Publications1
Metal bindingi17Magnesium 21 Publication1
Binding sitei17Substrate1 Publication1
Sitei148Important for interaction with ssb1 Publication1
Binding sitei165Substrate1 Publication1
Sitei181Important for activity1 Publication1
Metal bindingi186Magnesium 21 Publication1
Sitei207Important for interaction with ssb1 Publication1
Sitei311Important for interaction with ssb1 Publication1
Sitei338Important for interaction with ssb1 Publication1

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
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG10926-MONOMER.
ECOL316407:JW1993-MONOMER.
MetaCyc:EG10926-MONOMER.
BRENDAi3.1.11.1. 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
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10926. sbcB.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi148R → A: Strongly reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi150E → A: About 2-fold increased ssb-binding. Weakly increased ssb-independent and ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi181H → A: Residual nuclease activity. 1 Publication1
Mutagenesisi207Y → A: Strongly reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi227K → A: 7-fold reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi311Q → A: 2-fold reduced ssb-binding. Weakly reduced ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi316R → A: Strongly reduced ssb-binding. Strongly reduced ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi318E → A: About 2-fold increased ssb-binding. No effect on ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi319D → A: 2-fold reduced ssb-binding. No effect on ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi327R → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi331L → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi338R → A: 3-fold reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi448Q → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication1
Mutagenesisi452Q → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000871101 – 475Exodeoxyribonuclease IAdd BLAST475

Proteomic databases

PaxDbiP04995.
PRIDEiP04995.

Interactioni

Subunit structurei

Monomer (PubMed:23609540). Interacts with ssb (via C-terminus); this interaction stimulates the exonuclease activity by recruiting the enzyme to its substrate (PubMed:18591666, PubMed:20018747).3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei18Interaction with single-stranded DNA1 Publication1
Sitei66Interaction with single-stranded DNA1 Publication1
Sitei113Interaction with single-stranded DNA1 Publication1
Sitei124Interaction with single-stranded DNA1 Publication1
Sitei128Interaction with single-stranded DNA1 Publication1
Sitei142Interaction with single-stranded DNA1 Publication1
Sitei164Interaction with single-stranded DNACombined sources1 Publication1
Sitei214Interaction with single-stranded DNA1 Publication1
Sitei257Interaction with single-stranded DNACombined sources1 Publication1
Sitei284Interaction with single-stranded DNA1 Publication1
Sitei304Interaction with single-stranded DNACombined sources1 Publication1
Sitei368Interaction with single-stranded DNA1 Publication1
Sitei371Interaction with single-stranded DNA1 Publication1

Protein-protein interaction databases

BioGridi4260414. 101 interactors.
DIPiDIP-10827N.
IntActiP04995. 6 interactors.
MINTiMINT-1241098.
STRINGi511145.b2011.

Structurei

Secondary structure

1475
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 21Combined sources12
Turni23 – 25Combined sources3
Beta strandi28 – 36Combined sources9
Beta strandi47 – 51Combined sources5
Helixi61 – 67Combined sources7
Helixi71 – 77Combined sources7
Helixi81 – 92Combined sources12
Beta strandi97 – 103Combined sources7
Turni104 – 107Combined sources4
Helixi108 – 118Combined sources11
Helixi125 – 127Combined sources3
Helixi129 – 131Combined sources3
Beta strandi133 – 136Combined sources4
Helixi137 – 147Combined sources11
Beta strandi160 – 162Combined sources3
Helixi166 – 172Combined sources7
Helixi185 – 200Combined sources16
Helixi202 – 210Combined sources9
Helixi214 – 219Combined sources6
Turni223 – 226Combined sources4
Beta strandi229 – 232Combined sources4
Helixi234 – 236Combined sources3
Helixi238 – 240Combined sources3
Beta strandi243 – 251Combined sources9
Beta strandi258 – 263Combined sources6
Helixi269 – 273Combined sources5
Helixi276 – 285Combined sources10
Helixi287 – 289Combined sources3
Beta strandi298 – 302Combined sources5
Helixi303 – 305Combined sources3
Beta strandi308 – 311Combined sources4
Helixi312 – 314Combined sources3
Helixi317 – 323Combined sources7
Helixi327 – 339Combined sources13
Helixi343 – 346Combined sources4
Helixi363 – 365Combined sources3
Helixi367 – 369Combined sources3
Helixi374 – 385Combined sources12
Turni388 – 390Combined sources3
Turni391 – 393Combined sources3
Helixi402 – 414Combined sources13
Helixi416 – 418Combined sources3
Helixi421 – 434Combined sources14
Helixi437 – 453Combined sources17
Turni454 – 456Combined sources3
Helixi458 – 473Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1FXXX-ray2.40A1-475[»]
2QXFX-ray1.50A1-475[»]
3C94X-ray2.70A1-475[»]
3C95X-ray1.70A1-475[»]
3HL8X-ray1.55A1-475[»]
3HP9X-ray1.60A1-475[»]
4HCBX-ray2.00A/B1-475[»]
4HCCX-ray2.96A/B1-475[»]
4JRPX-ray1.95A/B1-475[»]
4JRQX-ray3.00A/B1-475[»]
4JS4X-ray3.10A/B1-475[»]
4JS5X-ray3.50A/B1-475[»]
ProteinModelPortaliP04995.
SMRiP04995.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04995.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini13 – 192ExonucleaseSequence analysisAdd BLAST180
Domaini202 – 355ExoI SH3-likePROSITE-ProRule annotationAdd BLAST154
Domaini358 – 475ExoI C-terminalPROSITE-ProRule annotationAdd BLAST118

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

Sequence similaritiesi

Contains 1 ExoI C-terminal domain.PROSITE-ProRule annotation
Contains 1 ExoI SH3-like domain.PROSITE-ProRule annotation
Contains 1 exonuclease domain.Sequence analysis

Phylogenomic databases

eggNOGiENOG4105CJB. Bacteria.
COG2925. LUCA.
HOGENOMiHOG000276591.
InParanoidiP04995.
KOiK01141.
OMAiRDRPAQF.
PhylomeDBiP04995.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR023607. Exodeoxyribonuclease_I.
IPR013620. Exonuc_X-T_C.
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR012337. RNaseH-like_dom.
[Graphical view]
PANTHERiPTHR11046:SF2. PTHR11046:SF2. 1 hit.
PfamiPF08411. Exonuc_X-T_C. 1 hit.
PF00929. RNase_T. 1 hit.
[Graphical view]
PIRSFiPIRSF000977. Exodeoxyribonuclease_I. 1 hit.
SMARTiSM00479. EXOIII. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS51785. EXOI_C. 1 hit.
PS51784. EXOI_SH3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P04995-1 [UniParc]FASTAAdd to basket

« Hide

        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
Length:475
Mass (Da):54,501
Last modified:February 1, 1994 - v2
Checksum:iA6A02AC17922C313
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti210 – 218Missing in AAA19938 (PubMed:3539937).Curated9
Sequence conflicti225Q → H in AAA19938 (PubMed:3539937).Curated1
Sequence conflicti343V → E in AAA19938 (PubMed:3539937).Curated1
Sequence conflicti475V → A in AAA19938 (PubMed:3539937).Curated1

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.
PIRiB64966. NCECX1.
RefSeqiNP_416515.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC75072; AAC75072; b2011.
BAA15839; BAA15839; BAA15839.
GeneIDi946529.
KEGGiecj:JW1993.
eco:b2011.
PATRICi32119357. VBIEscCol129921_2088.

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.
PIRiB64966. NCECX1.
RefSeqiNP_416515.1. NC_000913.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1FXXX-ray2.40A1-475[»]
2QXFX-ray1.50A1-475[»]
3C94X-ray2.70A1-475[»]
3C95X-ray1.70A1-475[»]
3HL8X-ray1.55A1-475[»]
3HP9X-ray1.60A1-475[»]
4HCBX-ray2.00A/B1-475[»]
4HCCX-ray2.96A/B1-475[»]
4JRPX-ray1.95A/B1-475[»]
4JRQX-ray3.00A/B1-475[»]
4JS4X-ray3.10A/B1-475[»]
4JS5X-ray3.50A/B1-475[»]
ProteinModelPortaliP04995.
SMRiP04995.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260414. 101 interactors.
DIPiDIP-10827N.
IntActiP04995. 6 interactors.
MINTiMINT-1241098.
STRINGi511145.b2011.

Proteomic databases

PaxDbiP04995.
PRIDEiP04995.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75072; AAC75072; b2011.
BAA15839; BAA15839; BAA15839.
GeneIDi946529.
KEGGiecj:JW1993.
eco:b2011.
PATRICi32119357. VBIEscCol129921_2088.

Organism-specific databases

EchoBASEiEB0919.
EcoGeneiEG10926. sbcB.

Phylogenomic databases

eggNOGiENOG4105CJB. Bacteria.
COG2925. LUCA.
HOGENOMiHOG000276591.
InParanoidiP04995.
KOiK01141.
OMAiRDRPAQF.
PhylomeDBiP04995.

Enzyme and pathway databases

BioCyciEcoCyc:EG10926-MONOMER.
ECOL316407:JW1993-MONOMER.
MetaCyc:EG10926-MONOMER.
BRENDAi3.1.11.1. 2026.

Miscellaneous databases

EvolutionaryTraceiP04995.
PROiP04995.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
InterProiIPR023607. Exodeoxyribonuclease_I.
IPR013620. Exonuc_X-T_C.
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR012337. RNaseH-like_dom.
[Graphical view]
PANTHERiPTHR11046:SF2. PTHR11046:SF2. 1 hit.
PfamiPF08411. Exonuc_X-T_C. 1 hit.
PF00929. RNase_T. 1 hit.
[Graphical view]
PIRSFiPIRSF000977. Exodeoxyribonuclease_I. 1 hit.
SMARTiSM00479. EXOIII. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS51785. EXOI_C. 1 hit.
PS51784. EXOI_SH3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiEX1_ECOLI
AccessioniPrimary (citable) accession number: P04995
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: February 1, 1994
Last modified: November 2, 2016
This is version 157 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.