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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi15 – 151Magnesium 15 Publications
Metal bindingi17 – 171Magnesium 21 Publication
Binding sitei17 – 171Substrate1 Publication
Sitei18 – 181Interaction with single-stranded DNA1 Publication
Sitei66 – 661Interaction with single-stranded DNA1 Publication
Sitei113 – 1131Interaction with single-stranded DNA1 Publication
Sitei124 – 1241Interaction with single-stranded DNA1 Publication
Sitei128 – 1281Interaction with single-stranded DNA1 Publication
Sitei142 – 1421Interaction with single-stranded DNA1 Publication
Sitei148 – 1481Important for interaction with ssb1 Publication
Sitei164 – 1641Interaction with single-stranded DNACombined sources1 Publication
Binding sitei165 – 1651Substrate1 Publication
Sitei181 – 1811Important for activity1 Publication
Metal bindingi186 – 1861Magnesium 21 Publication
Sitei207 – 2071Important for interaction with ssb1 Publication
Sitei214 – 2141Interaction with single-stranded DNA1 Publication
Sitei257 – 2571Interaction with single-stranded DNACombined sources1 Publication
Sitei284 – 2841Interaction with single-stranded DNA1 Publication
Sitei304 – 3041Interaction with single-stranded DNACombined sources1 Publication
Sitei311 – 3111Important for interaction with ssb1 Publication
Sitei338 – 3381Important for interaction with ssb1 Publication
Sitei368 – 3681Interaction with single-stranded DNA1 Publication
Sitei371 – 3711Interaction with single-stranded DNA1 Publication

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: GO_Central
  • exodeoxyribonuclease I activity Source: UniProtKB
  • magnesium ion binding Source: UniProtKB
  • single-stranded DNA binding Source: UniProtKB

GO - Biological processi

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10926. sbcB.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi148 – 1481R → A: Strongly reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication
Mutagenesisi150 – 1501E → A: About 2-fold increased ssb-binding. Weakly increased ssb-independent and ssb-dependent nuclease activity. 1 Publication
Mutagenesisi181 – 1811H → A: Residual nuclease activity. 1 Publication
Mutagenesisi207 – 2071Y → A: Strongly reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication
Mutagenesisi227 – 2271K → A: 7-fold reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication
Mutagenesisi311 – 3111Q → A: 2-fold reduced ssb-binding. Weakly reduced ssb-dependent nuclease activity. 1 Publication
Mutagenesisi316 – 3161R → A: Strongly reduced ssb-binding. Strongly reduced ssb-dependent nuclease activity. 1 Publication
Mutagenesisi318 – 3181E → A: About 2-fold increased ssb-binding. No effect on ssb-dependent nuclease activity. 1 Publication
Mutagenesisi319 – 3191D → A: 2-fold reduced ssb-binding. No effect on ssb-dependent nuclease activity. 1 Publication
Mutagenesisi327 – 3271R → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication
Mutagenesisi331 – 3311L → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication
Mutagenesisi338 – 3381R → A: 3-fold reduced ssb-binding. Reduced ssb-dependent nuclease activity. 1 Publication
Mutagenesisi448 – 4481Q → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication
Mutagenesisi452 – 4521Q → A: No effect on ssb-binding and on ssb-dependent nuclease activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 475475Exodeoxyribonuclease IPRO_0000087110Add
BLAST

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

Protein-protein interaction databases

DIPiDIP-10827N.
IntActiP04995. 6 interactions.
MINTiMINT-1241098.
STRINGi511145.b2011.

Structurei

Secondary structure

1
475
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi10 – 2112Combined sources
Turni23 – 253Combined sources
Beta strandi28 – 369Combined sources
Beta strandi47 – 515Combined sources
Helixi61 – 677Combined sources
Helixi71 – 777Combined sources
Helixi81 – 9212Combined sources
Beta strandi97 – 1037Combined sources
Turni104 – 1074Combined sources
Helixi108 – 11811Combined sources
Helixi125 – 1273Combined sources
Helixi129 – 1313Combined sources
Beta strandi133 – 1364Combined sources
Helixi137 – 14711Combined sources
Beta strandi160 – 1623Combined sources
Helixi166 – 1727Combined sources
Helixi185 – 20016Combined sources
Helixi202 – 2109Combined sources
Helixi214 – 2196Combined sources
Turni223 – 2264Combined sources
Beta strandi229 – 2324Combined sources
Helixi234 – 2363Combined sources
Helixi238 – 2403Combined sources
Beta strandi243 – 2519Combined sources
Beta strandi258 – 2636Combined sources
Helixi269 – 2735Combined sources
Helixi276 – 28510Combined sources
Helixi287 – 2893Combined sources
Beta strandi298 – 3025Combined sources
Helixi303 – 3053Combined sources
Beta strandi308 – 3114Combined sources
Helixi312 – 3143Combined sources
Helixi317 – 3237Combined sources
Helixi327 – 33913Combined sources
Helixi343 – 3464Combined sources
Helixi363 – 3653Combined sources
Helixi367 – 3693Combined sources
Helixi374 – 38512Combined sources
Turni388 – 3903Combined sources
Turni391 – 3933Combined sources
Helixi402 – 41413Combined sources
Helixi416 – 4183Combined sources
Helixi421 – 43414Combined sources
Helixi437 – 45317Combined sources
Turni454 – 4563Combined sources
Helixi458 – 47316Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 8-475.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04995.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini13 – 192180ExonucleaseSequence AnalysisAdd
BLAST
Domaini212 – 473262Exonuclease C-terminalSequence AnalysisAdd
BLAST

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 exonuclease C-terminal domain.Sequence Analysis
Contains 1 exonuclease domain.Sequence Analysis

Phylogenomic databases

eggNOGiCOG2925.
HOGENOMiHOG000276591.
InParanoidiP04995.
KOiK01141.
OMAiRDRPAQF.
OrthoDBiEOG6MWN7F.
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]
PfamiPF08411. Exonuc_X-T_C. 1 hit.
PF00929. RNase_T. 1 hit.
[Graphical view]
PIRSFiPIRSF000977. Exodeoxyribonuclease_I. 1 hit.
SUPFAMiSSF53098. SSF53098. 1 hit.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti210 – 2189Missing in AAA19938 (PubMed:3539937).Curated
Sequence conflicti225 – 2251Q → H in AAA19938 (PubMed:3539937).Curated
Sequence conflicti343 – 3431V → E in AAA19938 (PubMed:3539937).Curated
Sequence conflicti475 – 4751V → A in AAA19938 (PubMed:3539937).Curated

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.
KEGGieco: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
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. Positions 8-475.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-10827N.
IntActiP04995. 6 interactions.
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.
KEGGieco:b2011.
PATRICi32119357. VBIEscCol129921_2088.

Organism-specific databases

EchoBASEiEB0919.
EcoGeneiEG10926. sbcB.

Phylogenomic databases

eggNOGiCOG2925.
HOGENOMiHOG000276591.
InParanoidiP04995.
KOiK01141.
OMAiRDRPAQF.
OrthoDBiEOG6MWN7F.
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]
PfamiPF08411. Exonuc_X-T_C. 1 hit.
PF00929. RNase_T. 1 hit.
[Graphical view]
PIRSFiPIRSF000977. Exodeoxyribonuclease_I. 1 hit.
SUPFAMiSSF53098. SSF53098. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Determination of the nucleotide sequence for the exonuclease I structural gene (sbcB) of Escherichia coli K12."
    Phillips G.J., Kushner S.R.
    J. Biol. Chem. 262:455-459(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-12.
    Strain: K12.
  2. "Automated multiplex sequencing of the E.coli genome."
    Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M.
    Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / BHB2600.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. 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. "DNA deoxyribophosphodiesterase of Escherichia coli is associated with exonuclease I."
    Sandigursky M., Franklin W.A.
    Nucleic Acids Res. 20:4699-4703(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A DRPASE.
  7. "Structure of Escherichia coli exonuclease I suggests how processivity is achieved."
    Breyer W.A., Matthews B.W.
    Nat. Struct. Biol. 7:1125-1128(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, DOMAIN.
    Strain: K12 / DH5-alpha1 Publication.
  8. "Structure of Escherichia coli exonuclease I in complex with thymidine 5'-monophosphate."
    Busam R.D.
    Acta Crystallogr. D 64:206-210(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH DTMP PRODUCT AND MAGNESIUM, COFACTOR, DOMAIN.
    Strain: K121 Publication.
  9. "Structural basis of Escherichia coli single-stranded DNA-binding protein stimulation of exonuclease I."
    Lu D., Keck J.L.
    Proc. Natl. Acad. Sci. U.S.A. 105:9169-9174(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF APO FORM AND IN COMPLEX WITH SSB TAIL PEPTIDE AND MAGNESIUM, CATALYTIC ACTIVITY, COFACTOR, INTERACTION WITH SSB, DOMAIN, SITES, MUTAGENESIS OF ARG-148; GLU-150; TYR-207; LYS-227; GLN-311; ARG-316; GLU-318; ASP-319; ARG-327; LEU-331; ARG-338; GLN-448 AND GLN-452.
  10. "Small-molecule tools for dissecting the roles of SSB/protein interactions in genome maintenance."
    Lu D., Bernstein D.A., Satyshur K.A., Keck J.L.
    Proc. Natl. Acad. Sci. U.S.A. 107:633-638(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEXES WITH INHIBITORS AND MAGNESIUM, CATALYTIC ACTIVITY, COFACTOR, INTERACTION WITH SSB, SITE.
  11. "The structures of Escherichia coli exonuclease I in complex with the single strand DNA."
    Qiu R., Lou T., Wei J., Liu M., Gu S., Tang R., Ji C., Gong W.
    Submitted (SEP-2012) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEXES WITH SINGLE-STRANDED DNA SUBSTRATES AND ZINC.
  12. "Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion."
    Korada S.K., Johns T.D., Smith C.E., Jones N.D., McCabe K.A., Bell C.E.
    Nucleic Acids Res. 41:5887-5897(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEXES WITH SINGLE-STRANDED DNA SUBSTRATES AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, SUBUNIT, DOMAIN, MUTAGENESIS OF HIS-181.
    Strain: K121 Publication.

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: July 22, 2015
This is version 149 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

External Data

Dasty 3

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 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.