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P06229

- EXO5_BPT5

UniProt

P06229 - EXO5_BPT5

Protein

Exodeoxyribonuclease

Gene

D15

Organism
Enterobacteria phage T5 (Bacteriophage T5)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 100 (01 Oct 2014)
      Sequence version 3 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    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 activityi

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

    Cofactori

    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.1 Publication

    pH dependencei

    Optimum pH is 9.3 for the exonuclease activity, 5.5 for endonuclease activity.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi26 – 261Divalent metal cation 1Curated
    Metal bindingi68 – 681Divalent metal cation 1Curated
    Active sitei83 – 831Proton acceptor (Probable); for exonuclease activityCurated
    Metal bindingi128 – 1281Divalent metal cation 1Curated
    Metal bindingi131 – 1311Divalent metal cation 1Curated
    Metal bindingi153 – 1531Divalent metal cation 1Curated
    Metal bindingi153 – 1531Divalent metal cation 2Curated
    Metal bindingi155 – 1551Divalent metal cation 2Curated
    Metal bindingi201 – 2011Divalent metal cation 2Curated
    Metal bindingi204 – 2041Divalent metal cation 2Curated

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. endonuclease activity Source: UniProtKB-KW
    3. exonuclease activity Source: UniProtKB-KW
    4. metal ion binding Source: UniProtKB-KW

    Keywords - Molecular functioni

    Endonuclease, Exonuclease, Hydrolase, Nuclease

    Keywords - Ligandi

    DNA-binding, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exodeoxyribonuclease (EC:3.1.11.3)
    Alternative name(s):
    5'-exonuclease
    T5FEN
    Gene namesi
    Name:D15
    OrganismiEnterobacteria phage T5 (Bacteriophage T5)
    Taxonomic identifieri10726 [NCBI]
    Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesSiphoviridaeT5likevirus
    Virus hostiEscherichia coli [TaxID: 562]
    ProteomesiUP000002107: Genome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi83 – 831K → A: No exonuclease activity, retains full endonuclease activity on a flap structure. Binds DNA pseudo-Y substrates with a dissociation constant of 200 nM. 2 Publications
    Mutagenesisi128 – 1303EAD → QAN: Loss of both exo- and endonuclease activity, still binds DNA. 1 Publication
    Mutagenesisi196 – 1961K → A: 10% exonuclease activity, little change in endonuclease activity. Binds DNA pseudo-Y substrates with a dissociation constant of 200 nM. 2 Publications
    Mutagenesisi201 – 2044DLGD → ILGS: Retains most endo- but very little exonuclease activity; binds pseudo-Y substrate more tightly than wt. 1 Publication
    Mutagenesisi201 – 2044DLGD → RLGP or RLGR: Retains most endonuclease but complete loss of exonuclease activity; binds pseudo-Y substrate more tightly than wt. 1 Publication
    Mutagenesisi215 – 2151K → A: Wild-type exo- and endonuclease activities. Binds DNA pseudo-Y substrates with a dissociation constant of 50 nM. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed; by host
    Chaini2 – 291290ExodeoxyribonucleasePRO_0000165217Add
    BLAST

    Structurei

    Secondary structure

    1
    291
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi21 – 266
    Helixi27 – 3711
    Beta strandi39 – 413
    Helixi44 – 5714
    Beta strandi60 – 667
    Helixi73 – 786
    Turni80 – 834
    Helixi84 – 918
    Helixi95 – 11521
    Turni116 – 1183
    Helixi129 – 14012
    Helixi141 – 1433
    Beta strandi147 – 1504
    Helixi154 – 1596
    Beta strandi162 – 1687
    Turni169 – 1724
    Beta strandi173 – 1753
    Helixi177 – 1793
    Helixi180 – 1845
    Beta strandi185 – 1884
    Helixi189 – 19911
    Helixi202 – 2043
    Helixi214 – 22411
    Helixi227 – 2337
    Helixi241 – 2477
    Helixi250 – 26011
    Helixi262 – 27110
    Helixi275 – 28814

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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[»]
    ProteinModelPortaliP06229.
    SMRiP06229. Positions 20-291.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP06229.

    Family & Domainsi

    Sequence similaritiesi

    Contains 1 5'-3' exonuclease domain.Curated

    Family and domain databases

    Gene3Di3.40.50.1010. 1 hit.
    InterProiIPR020046. 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]
    PfamiPF01367. 5_3_exonuc. 1 hit.
    PF02739. 5_3_exonuc_N. 1 hit.
    [Graphical view]
    SMARTiSM00475. 53EXOc. 1 hit.
    SM00279. HhH2. 1 hit.
    [Graphical view]
    SUPFAMiSSF47807. SSF47807. 1 hit.
    SSF88723. SSF88723. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P06229-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSKSWGKFIE EEEAEMASRR NLMIVDGTNL GFRFKHNNSK KPFASSYVST    50
    IQSLAKSYSA RTTIVLGDKG KSVFRLEHLP EYKGNRDEKY AQRTEEEKAL 100
    DEQFFEYLKD AFELCKTTFP TFTIRGVEAD DMAAYIVKLI GHLYDHVWLI 150
    STDGDWDTLL TDKVSRFSFT TRREYHLRDM YEHHNVDDVE QFISLKAIMG 200
    DLGDNIRGVE GIGAKRGYNI IREFGNVLDI IDQLPLPGKQ KYIQNLNASE 250
    ELLFRNLILV DLPTYCVDAI AAVGQDVLDK FTKDILEIAE Q 291
    Length:291
    Mass (Da):33,448
    Last modified:January 23, 2007 - v3
    Checksum:i234C9564E491B4E9
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY543070 Genomic DNA. Translation: AAS77176.1.
    PIRiA23610. NCBPT5.
    RefSeqiYP_006958.1. NC_005859.1.

    Genome annotation databases

    GeneIDi2777611.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY543070 Genomic DNA. Translation: AAS77176.1 .
    PIRi A23610. NCBPT5.
    RefSeqi YP_006958.1. NC_005859.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1EXN X-ray 2.50 A/B 2-291 [» ]
    1J5F model - A 20-289 [» ]
    1UT5 X-ray 2.75 A/B 2-291 [» ]
    1UT8 X-ray 2.75 A/B 2-291 [» ]
    1XO1 X-ray 2.50 A/B 1-291 [» ]
    ProteinModelPortali P06229.
    SMRi P06229. Positions 20-291.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 2777611.

    Miscellaneous databases

    EvolutionaryTracei P06229.

    Family and domain databases

    Gene3Di 3.40.50.1010. 1 hit.
    InterProi IPR020046. 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 ]
    Pfami PF01367. 5_3_exonuc. 1 hit.
    PF02739. 5_3_exonuc_N. 1 hit.
    [Graphical view ]
    SMARTi SM00475. 53EXOc. 1 hit.
    SM00279. HhH2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF47807. SSF47807. 1 hit.
    SSF88723. SSF88723. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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.

    Entry informationi

    Entry nameiEXO5_BPT5
    AccessioniPrimary (citable) accession number: P06229
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1988
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 100 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3