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P06229

- EXO5_BPT5

UniProt

P06229 - EXO5_BPT5

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Protein

Exodeoxyribonuclease

Gene

D15

Organism
Enterobacteria phage T5 (Bacteriophage T5)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli

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

Mg2+1 PublicationNote: Divalent metal cations, probably Mg(2+). 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 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; for exonuclease activity ProbableCurated
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
Complete GO annotation...

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. 1 Publication
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. 1 Publication
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. 1 Publication

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 – 266Combined sources
Helixi27 – 3711Combined sources
Beta strandi39 – 413Combined sources
Helixi44 – 5714Combined sources
Beta strandi60 – 667Combined sources
Helixi73 – 786Combined sources
Turni80 – 834Combined sources
Helixi84 – 918Combined sources
Helixi95 – 11521Combined sources
Turni116 – 1183Combined sources
Helixi129 – 14012Combined sources
Helixi141 – 1433Combined sources
Beta strandi147 – 1504Combined sources
Helixi154 – 1596Combined sources
Beta strandi162 – 1687Combined sources
Turni169 – 1724Combined sources
Beta strandi173 – 1753Combined sources
Helixi177 – 1793Combined sources
Helixi180 – 1845Combined sources
Beta strandi185 – 1884Combined sources
Helixi189 – 19911Combined sources
Helixi202 – 2043Combined sources
Helixi214 – 22411Combined sources
Helixi227 – 2337Combined sources
Helixi241 – 2477Combined sources
Helixi250 – 26011Combined sources
Helixi262 – 27110Combined sources
Helixi275 – 28814Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MSKSWGKFIE EEEAEMASRR NLMIVDGTNL GFRFKHNNSK KPFASSYVST
60 70 80 90 100
IQSLAKSYSA RTTIVLGDKG KSVFRLEHLP EYKGNRDEKY AQRTEEEKAL
110 120 130 140 150
DEQFFEYLKD AFELCKTTFP TFTIRGVEAD DMAAYIVKLI GHLYDHVWLI
160 170 180 190 200
STDGDWDTLL TDKVSRFSFT TRREYHLRDM YEHHNVDDVE QFISLKAIMG
210 220 230 240 250
DLGDNIRGVE GIGAKRGYNI IREFGNVLDI IDQLPLPGKQ KYIQNLNASE
260 270 280 290
ELLFRNLILV DLPTYCVDAI AAVGQDVLDK FTKDILEIAE Q
Length:291
Mass (Da):33,448
Last modified:January 23, 2007 - v3
Checksum:i234C9564E491B4E9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 102 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