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Protein

T5 flap endonuclease

Gene

D15

Organism
Escherichia phage T5 (Enterobacteria phage T5)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Metal bindingi26Divalent metal cation 12 Publications1
Metal bindingi68Divalent metal cation 12 Publications1
Active sitei83Proton acceptor; for exonuclease activityCurated1
Metal bindingi128Divalent metal cation 12 Publications1
Metal bindingi131Divalent metal cation 12 Publications1
Metal bindingi153Divalent metal cation 12 Publications1
Metal bindingi153Divalent metal cation 22 Publications1
Metal bindingi155Divalent metal cation 22 Publications1
Metal bindingi201Divalent metal cation 22 Publications1
Metal bindingi204Divalent metal cation 22 Publications1

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

Keywordsi

Molecular functionDNA-binding, Endonuclease, Exonuclease, Hydrolase, Nuclease
Biological processDNA replication, Viral DNA replication
LigandMetal-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 stageCaudoviralesSiphoviridaeT5virus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000002141 Componenti: Genome
  • UP000002107 Componenti: Genome
  • UP000002503 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi33R → A: 10 fold increase in the dissociation constant for pseudo-Y binding. 3 fold increase in the dissociation constant for 5'overhangs binding. 1 Publication1
Mutagenesisi82Y → F: 3.5-fold decrease in binding affinity for DNA. No effect on endonuclease and exonuclease activities. 1 Publication1
Mutagenesisi83K → 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 Publication1
Mutagenesisi128 – 130EAD → QAN: Loss of both exo- and endonuclease activity, still binds DNA. 1 Publication3
Mutagenesisi172R → A: 10 fold increase in the dissociation constant for pseudo-Y binding. No effect on 5'overhangs binding. 1 Publication1
Mutagenesisi196K → A: 10% exonuclease activity, little change in endonuclease activity. Binds DNA pseudo-Y substrates with a dissociation constant of 200 nM. 1 Publication1
Mutagenesisi201 – 204DLGD → ILGS: Retains most endo- but very little exonuclease activity; binds pseudo-Y substrate more tightly than wt. 1 Publication4
Mutagenesisi201 – 204DLGD → RLGP or RLGR: Retains most endonuclease but complete loss of exonuclease activity; binds pseudo-Y substrate more tightly than wt. 1 Publication4
Mutagenesisi215K → A: 10 fold increase in the dissociation constant for pseudo-Y binding. Drastic increase in the dissociation constant for 5'overhangs binding. 1 Publication1
Mutagenesisi215K → A: Wild-type exo- and endonuclease activities. Binds DNA pseudo-Y substrates with a dissociation constant of 50 nM. 1 Publication1
Mutagenesisi216R → A: 100 fold increase in the dissociation constant for pseudo-Y binding. Drastic increase in the dissociation constant for 5'overhangs binding. 1 Publication1
Mutagenesisi241K → A: 10 fold increase in the dissociation constant for pseudo-Y binding. 10 fold increase in the dissociation constant for 5'overhangs binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved; by host1 Publication
ChainiPRO_00001652172 – 291T5 flap endonucleaseAdd BLAST290

Expressioni

Inductioni

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

Keywords - Developmental stagei

Early protein

Structurei

Secondary structure

1291
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP06229
SMRiP06229
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06229

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini190 – 2635'-3' exonucleaseSequence analysisAdd BLAST74

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi10 – 15Poly-GluSequence analysis6

Phylogenomic databases

KOiK18950
OrthoDBiVOG090000FN

Family and domain databases

InterProiView protein in InterPro
IPR020046 5-3_exonucl_a-hlix_arch_N
IPR036279 5-3_exonuclease_C_sf
IPR002421 5-3_exonuclease_N
IPR020045 DNA_polI_H3TH
IPR038969 FEN_bact-like
IPR008918 HhH2
IPR029060 PIN-like_dom_sf
PANTHERiPTHR42646 PTHR42646, 1 hit
PfamiView protein in Pfam
PF01367 5_3_exonuc, 1 hit
PF02739 5_3_exonuc_N, 1 hit
SMARTiView protein in SMART
SM00475 53EXOc, 1 hit
SM00279 HhH2, 1 hit
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 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

Similar proteinsi

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
PDB 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[»]
5HMLX-ray1.48A/B20-291[»]
5HMMX-ray1.50A/B20-290[»]
5HNKX-ray2.22A/B20-291[»]
5HP4X-ray1.86A20-291[»]
ProteinModelPortaliP06229
SMRiP06229
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi2777611
KEGGivg:2777611

Phylogenomic databases

KOiK18950
OrthoDBiVOG090000FN

Miscellaneous databases

EvolutionaryTraceiP06229

Family and domain databases

InterProiView protein in InterPro
IPR020046 5-3_exonucl_a-hlix_arch_N
IPR036279 5-3_exonuclease_C_sf
IPR002421 5-3_exonuclease_N
IPR020045 DNA_polI_H3TH
IPR038969 FEN_bact-like
IPR008918 HhH2
IPR029060 PIN-like_dom_sf
PANTHERiPTHR42646 PTHR42646, 1 hit
PfamiView protein in Pfam
PF01367 5_3_exonuc, 1 hit
PF02739 5_3_exonuc_N, 1 hit
SMARTiView protein in SMART
SM00475 53EXOc, 1 hit
SM00279 HhH2, 1 hit
SUPFAMiSSF47807 SSF47807, 1 hit
SSF88723 SSF88723, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiEXO5_BPT5
AccessioniPrimary (citable) accession number: P06229
Secondary accession number(s): Q5DMH3, Q66LT5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: January 23, 2007
Last modified: June 20, 2018
This is version 125 of the entry and version 3 of the sequence. See 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
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