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P06229 (EXO5_BPT5) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 99. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Exodeoxyribonuclease

EC=3.1.11.3
Alternative name(s):
5'-exonuclease
T5FEN
Gene names
Name:D15
OrganismEnterobacteria phage T5 (Bacteriophage T5) [Reference proteome]
Taxonomic identifier10726 [NCBI]
Taxonomic lineageVirusesdsDNA viruses, no RNA stageCaudoviralesSiphoviridaeT5likevirus
Virus hostEscherichia coli [TaxID: 562]

Protein attributes

Sequence length291 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

5'-exonucleolytic degradation of double-stranded (ds) DNA. Can also cleave bifurcated nucleic acids such as flap and pseudo-Y substrates in a structure-specific manner. This requires free 5' single-stranded (ss) ends and cleaves at the ds/ss junction. Binds DNA pseudo-Y substrates with a dissociation constant of 5 nM.

Catalytic activity

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

Cofactor

Divalent cations, probably magnesium. In vitro low metal concentrations selectively stimulate the endonuclease reaction. There are 2 metal binding sites of differing affinity. Endonuclease activity is suggested to require only of the first cation, whereas exonuclease activity is suggested to require binding of both. Metal ions enhance substrate binding. Ref.5

Sequence similarities

Contains 1 5'-3' exonuclease domain.

Biophysicochemical properties

pH dependence:

Optimum pH is 9.3 for the exonuclease activity, 5.5 for endonuclease activity. Ref.4

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed; by host
Chain2 – 291290Exodeoxyribonuclease
PRO_0000165217

Sites

Active site831Proton acceptor (Probable); for exonuclease activity
Metal binding261Divalent metal cation 1 Probable
Metal binding681Divalent metal cation 1 Probable
Metal binding1281Divalent metal cation 1 Probable
Metal binding1311Divalent metal cation 1 Probable
Metal binding1531Divalent metal cation 1 Probable
Metal binding1531Divalent metal cation 2 Probable
Metal binding1551Divalent metal cation 2 Probable
Metal binding2011Divalent metal cation 2 Probable
Metal binding2041Divalent metal cation 2 Probable

Experimental info

Mutagenesis831K → A: No exonuclease activity, retains full endonuclease activity on a flap structure. Binds DNA pseudo-Y substrates with a dissociation constant of 200 nM. Ref.4
Mutagenesis128 – 1303EAD → QAN: Loss of both exo- and endonuclease activity, still binds DNA. Ref.5
Mutagenesis1961K → A: 10% exonuclease activity, little change in endonuclease activity. Binds DNA pseudo-Y substrates with a dissociation constant of 200 nM. Ref.4
Mutagenesis201 – 2044DLGD → ILGS: Retains most endo- but very little exonuclease activity; binds pseudo-Y substrate more tightly than wt. Ref.5
Mutagenesis201 – 2044DLGD → RLGP or RLGR: Retains most endonuclease but complete loss of exonuclease activity; binds pseudo-Y substrate more tightly than wt. Ref.5
Mutagenesis2151K → A: Wild-type exo- and endonuclease activities. Binds DNA pseudo-Y substrates with a dissociation constant of 50 nM. Ref.4

Secondary structure

................................................ 291
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P06229 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 234C9564E491B4E9

FASTA29133,448
        10         20         30         40         50         60 
MSKSWGKFIE EEEAEMASRR NLMIVDGTNL GFRFKHNNSK KPFASSYVST IQSLAKSYSA 

        70         80         90        100        110        120 
RTTIVLGDKG KSVFRLEHLP EYKGNRDEKY AQRTEEEKAL DEQFFEYLKD AFELCKTTFP 

       130        140        150        160        170        180 
TFTIRGVEAD DMAAYIVKLI GHLYDHVWLI STDGDWDTLL TDKVSRFSFT TRREYHLRDM 

       190        200        210        220        230        240 
YEHHNVDDVE QFISLKAIMG DLGDNIRGVE GIGAKRGYNI IREFGNVLDI IDQLPLPGKQ 

       250        260        270        280        290 
KYIQNLNASE ELLFRNLILV DLPTYCVDAI AAVGQDVLDK FTKDILEIAE Q 

« Hide

References

« Hide 'large scale' references
[1]"Cloning and DNA sequence of the 5'-exonuclease gene of bacteriophage T5."
Kaliman A.V., Krutilina A.I., Kryukov V.M., Bayev A.A.
FEBS Lett. 195:61-64(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Bacteriophage T5 complete genome."
Ksenzenko V.N., Kaliman A.V., Krutilina A.I., Shlyapnikov M.G.
Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease."
Ceska T.A., Sayers J.R., Stier G., Suck D.
Nature 382:90-93(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), ENDONUCLEASE ACTIVITY.
[4]"Mutagenesis of conserved lysine residues in bacteriophage T5 5'-3' exonuclease suggests separate mechanisms of endo- and exonucleolytic cleavage."
Garforth S.J., Ceska T.A., Suck D., Sayers J.R.
Proc. Natl. Acad. Sci. U.S.A. 96:38-43(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF MUTANT ALA-83, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF LYS-83; LYS-196 AND LYS-215.
[5]"Roles of divalent metal ions in flap endonuclease-substrate interactions."
Feng M., Patel D., Dervan J.J., Ceska T., Suck D., Haq I., Sayers J.R.
Nat. Struct. Mol. Biol. 11:450-456(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) OF 2-290, COFACTOR, MUTAGENESIS OF 128-GLU--ASP-130 AND 201-ASP--ASP-204.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AY543070 Genomic DNA. Translation: AAS77176.1.
PIRNCBPT5. A23610.
RefSeqYP_006958.1. NC_005859.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1EXNX-ray2.50A/B2-291[»]
1J5Fmodel-A20-289[»]
1UT5X-ray2.75A/B2-291[»]
1UT8X-ray2.75A/B2-291[»]
1XO1X-ray2.50A/B1-291[»]
ProteinModelPortalP06229.
SMRP06229. Positions 20-291.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID2777611.

Family and domain databases

Gene3D3.40.50.1010. 1 hit.
InterProIPR020046. 5-3_exonucl_a-hlix_arch_N.
IPR020045. 5-3_exonuclease_C.
IPR002421. 5-3_exonuclease_N.
IPR008918. HhH2.
IPR029060. PIN_domain-like.
[Graphical view]
PfamPF01367. 5_3_exonuc. 1 hit.
PF02739. 5_3_exonuc_N. 1 hit.
[Graphical view]
SMARTSM00475. 53EXOc. 1 hit.
SM00279. HhH2. 1 hit.
[Graphical view]
SUPFAMSSF47807. SSF47807. 1 hit.
SSF88723. SSF88723. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP06229.

Entry information

Entry nameEXO5_BPT5
AccessionPrimary (citable) accession number: P06229
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 23, 2007
Last modified: July 9, 2014
This is version 99 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references