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P04995

- EX1_ECOLI

UniProt

P04995 - EX1_ECOLI

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Protein

Exodeoxyribonuclease I

Gene

sbcB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli

Functioni

Also functions as a DNA deoxyribophosphodiesterase that releases deoxyribose-phosphate moieties following the cleavage DNA at an apurinic/apyrimidinic (AP) site by either an AP endonuclease AP lyase.1 Publication

Catalytic activityi

Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.

GO - Molecular functioni

  1. exodeoxyribonuclease I activity Source: EcoCyc
  2. nucleic acid binding Source: InterPro

GO - Biological processi

  1. DNA catabolic process Source: EcoCyc
  2. DNA catabolic process, exonucleolytic Source: GOC
  3. DNA repair Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

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:3.1.11.1)
Short name:
Exonuclease I
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: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10926. sbcB.

PTM / Processingi

Molecule processing

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

Proteomic databases

PaxDbiP04995.
PRIDEiP04995.

Expressioni

Gene expression databases

GenevestigatoriP04995.

Interactioni

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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

Phylogenomic databases

eggNOGiCOG2925.
HOGENOMiHOG000276591.
InParanoidiP04995.
KOiK01141.
OMAiNFFDPYA.
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:
EMBL
GenBank
DDBJ
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.
YP_490253.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75072; AAC75072; b2011.
BAA15839; BAA15839; BAA15839.
GeneIDi12931420.
946529.
KEGGiecj:Y75_p1973.
eco:b2011.
PATRICi32119357. VBIEscCol129921_2088.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.
YP_490253.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
ProteinModelPortali P04995.
SMRi P04995. Positions 8-475.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-10827N.
IntActi P04995. 6 interactions.
MINTi MINT-1241098.
STRINGi 511145.b2011.

Proteomic databases

PaxDbi P04995.
PRIDEi P04995.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75072 ; AAC75072 ; b2011 .
BAA15839 ; BAA15839 ; BAA15839 .
GeneIDi 12931420.
946529.
KEGGi ecj:Y75_p1973.
eco:b2011.
PATRICi 32119357. VBIEscCol129921_2088.

Organism-specific databases

EchoBASEi EB0919.
EcoGenei EG10926. sbcB.

Phylogenomic databases

eggNOGi COG2925.
HOGENOMi HOG000276591.
InParanoidi P04995.
KOi K01141.
OMAi NFFDPYA.
OrthoDBi EOG6MWN7F.
PhylomeDBi P04995.

Enzyme and pathway databases

BioCyci EcoCyc:EG10926-MONOMER.
ECOL316407:JW1993-MONOMER.
MetaCyc:EG10926-MONOMER.
BRENDAi 3.1.11.1. 2026.

Miscellaneous databases

EvolutionaryTracei P04995.
PROi P04995.

Gene expression databases

Genevestigatori P04995.

Family and domain databases

Gene3Di 3.30.420.10. 1 hit.
InterProi IPR023607. Exodeoxyribonuclease_I.
IPR013620. Exonuc_X-T_C.
IPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR012337. RNaseH-like_dom.
[Graphical view ]
Pfami PF08411. Exonuc_X-T_C. 1 hit.
PF00929. RNase_T. 1 hit.
[Graphical view ]
PIRSFi PIRSF000977. Exodeoxyribonuclease_I. 1 hit.
SUPFAMi SSF53098. SSF53098. 1 hit.
ProtoNeti Search...

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.

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: October 29, 2014
This is version 142 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

External Data

Dasty 3