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Protein

T5 flap endonuclease

Gene

D15

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

Functioni

Flap endonuclease that probably plays a role in viral genome replication (PubMed:9874768) (PubMed:15077103). Catalyzes the exonucleolytic hydrolysis of blunt-ended double-stranded (ds) DNA (PubMed:9874768). This function may be used to process the Okazaki fragments from replicating DNA lagging strands (By similarity). Also catalyzses the endonucleolytic cleavage of 5'-bifurcated nucleic acids at the junction formed between single and double-stranded DNA (PubMed:9874768) (PubMed:15077103). This requires a free, single-stranded 5' end, with endonucleolytic hydrolysis occurring at the junction of double- and single-stranded DNA (PubMed:9874768). Binds DNA pseudo-Y substrates with a dissociation constant of 5 nM (PubMed:9874768).By similarity2 Publications

Catalytic activityi

Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates.2 Publications

Cofactori

Mg2+2 PublicationsNote: Divalent metal cations, probably Mg2+ (PubMed:12606565) (PubMed:15077103). In vitro low metal concentrations selectively stimulate the endonuclease reaction (PubMed:15077103). There are 2 metal binding sites of differing affinity (PubMed:15077103). Endonuclease activity is suggested to require only the first cation, whereas exonuclease activity is suggested to require binding of both (PubMed:15077103). Metal ions enhance substrate binding (PubMed:15077103).2 Publications

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 12 Publications
Metal bindingi68 – 681Divalent metal cation 12 Publications
Active sitei83 – 831Proton acceptor; for exonuclease activity ProbableCurated
Metal bindingi128 – 1281Divalent metal cation 12 Publications
Metal bindingi131 – 1311Divalent metal cation 12 Publications
Metal bindingi153 – 1531Divalent metal cation 12 Publications
Metal bindingi153 – 1531Divalent metal cation 22 Publications
Metal bindingi155 – 1551Divalent metal cation 22 Publications
Metal bindingi201 – 2011Divalent metal cation 22 Publications
Metal bindingi204 – 2041Divalent metal cation 22 Publications

GO - Molecular functioni

  • 5'-3' exonuclease activity Source: UniProtKB
  • 5'-flap endonuclease activity Source: UniProtKB
  • DNA binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA replication, Viral DNA replication

Keywords - Ligandi

DNA-binding, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
T5 flap endonuclease (EC:3.1.11.-Curated)
Short name:
T5FEN
Alternative name(s):
5'-3' exonucleaseCurated
Exodeoxyribonuclease1 Publication (EC:3.1.11.31 Publication)
Gene namesi
Name:D15
Synonyms:exo5Imported
ORF Names:T5.130Imported, T5p128Imported
OrganismiEscherichia phage T5 (Enterobacteria phage T5)
Taxonomic identifieri10726 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesSiphoviridaeT5likevirus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000002141 Componenti: Genome
  • UP000002107 Componenti: Genome
  • UP000002503 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi33 – 331R → A: 10 fold increase in the dissociation constant for pseudo-Y binding. 3 fold increase in the dissociation constant for 5'overhangs binding. 1 Publication
Mutagenesisi82 – 821Y → F: 3.5-fold decrease in binding affinity for DNA. No effect on endonuclease and exonuclease activities. 1 Publication
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
Mutagenesisi172 – 1721R → A: 10 fold increase in the dissociation constant for pseudo-Y binding. No effect on 5'overhangs binding. 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: 10 fold increase in the dissociation constant for pseudo-Y binding. Drastic increase in the dissociation constant for 5'overhangs binding. 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
Mutagenesisi216 – 2161R → A: 100 fold increase in the dissociation constant for pseudo-Y binding. Drastic increase in the dissociation constant for 5'overhangs binding. 1 Publication
Mutagenesisi241 – 2411K → A: 10 fold increase in the dissociation constant for pseudo-Y binding. 10 fold increase in the dissociation constant for 5'overhangs binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved; by host1 Publication
Chaini2 – 291290T5 flap endonucleasePRO_0000165217Add
BLAST

Expressioni

Inductioni

Expressed in the early phase of the viral replicative cycle.1 Publication

Keywords - Developmental stagei

Early protein

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

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini190 – 263745'-3' exonucleaseSequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi10 – 156Poly-GluSequence analysis

Sequence similaritiesi

Contains 1 5'-3' exonuclease domain.Sequence analysisCurated

Phylogenomic databases

KOiK18950.

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 cautioni

The sequence AAX12058.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY543070 Genomic DNA. Translation: AAS77176.1.
AY587007 Genomic DNA. Translation: AAX12058.1. Different initiation.
AY692264 Genomic DNA. Translation: AAU05267.1.
PIRiA23610. NCBPT5.
RefSeqiYP_006958.1. NC_005859.1.

Genome annotation databases

GeneIDi2777611.
KEGGivg:2777611.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY543070 Genomic DNA. Translation: AAS77176.1.
AY587007 Genomic DNA. Translation: AAX12058.1. Different initiation.
AY692264 Genomic DNA. Translation: AAU05267.1.
PIRiA23610. NCBPT5.
RefSeqiYP_006958.1. NC_005859.1.

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...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi2777611.
KEGGivg:2777611.

Phylogenomic databases

KOiK18950.

Miscellaneous databases

EvolutionaryTraceiP06229.

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.
ProtoNetiSearch...

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], INDUCTION.
    Strain: ATCC 11303-B5Imported.
  4. "Insights into bacteriophage T5 structure from analysis of its morphogenesis genes and protein components."
    Zivanovic Y., Confalonieri F., Ponchon L., Lurz R., Chami M., Flayhan A., Renouard M., Huet A., Decottignies P., Davidson A.R., Breyton C., Boulanger P.
    J. Virol. 88:1162-1174(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: St0 deletion mutant.
  5. "Properties of overexpressed phage T5 D15 exonuclease. Similarities with Escherichia coli DNA polymerase I 5'-3' exonuclease."
    Sayers J.R., Eckstein F.
    J. Biol. Chem. 265:18311-18317(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-20, CATALYTIC ACTIVITY.
  6. "Interactions of mutant and wild-type flap endonucleases with oligonucleotide substrates suggest an alternative model of DNA binding."
    Dervan J.J., Feng M., Patel D., Grasby J.A., Artymiuk P.J., Ceska T.A., Sayers J.R.
    Proc. Natl. Acad. Sci. U.S.A. 99:8542-8547(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ARG-33; ARG-172; LYS-215; ARG-216 AND LYS-241, DNA-BINDING.
  7. "A conserved tyrosine residue aids ternary complex formation, but not catalysis, in phage T5 flap endonuclease."
    Patel D., Tock M.R., Frary E., Feng M., Pickering T.J., Grasby J.A., Sayers J.R.
    J. Mol. Biol. 320:1025-1035(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF TYR-82.
  8. "Dynamic evidence for metal ion catalysis in the reaction mediated by a flap endonuclease."
    Tock M.R., Frary E., Sayers J.R., Grasby J.A.
    EMBO J. 22:995-1004(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: COFACTOR.
  9. "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).
  10. "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, FUNCTION, CATALYTIC ACTIVITY.
  11. "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, FUNCTION.

Entry informationi

Entry nameiEXO5_BPT5
AccessioniPrimary (citable) accession number: P06229
Secondary accession number(s): Q5DMH3, Q66LT5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 23, 2007
Last modified: July 6, 2016
This is version 113 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, Direct protein sequencing, Reference proteome

Documents

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

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 one 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.