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T5 flap endonuclease (T5FEN) (EC 3.1.11.-) (5'-3' exonuclease) (Exodeoxyribonuclease) (EC 3.1.11.3)

 EXO5_BPT5               Reviewed;         291 AA.
P06229; Q5DMH3; Q66LT5;
01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
20-JUN-2018, entry version 125.
RecName: Full=T5 flap endonuclease;
Short=T5FEN;
EC=3.1.11.- {ECO:0000305};
AltName: Full=5'-3' exonuclease {ECO:0000305};
AltName: Full=Exodeoxyribonuclease {ECO:0000303|PubMed:2211703};
EC=3.1.11.3 {ECO:0000269|PubMed:2211703};
Name=D15; Synonyms=exo5 {ECO:0000312|EMBL:AAX12058.1};
ORFNames=T5.130 {ECO:0000312|EMBL:AAS77176.1},
T5p128 {ECO:0000312|EMBL:AAU05267.1};
Escherichia phage T5 (Enterobacteria phage T5).
Viruses; dsDNA viruses, no RNA stage; Caudovirales; Siphoviridae;
T5virus.
NCBI_TaxID=10726;
NCBI_TaxID=562; Escherichia coli.
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3002857; DOI=10.1016/0014-5793(86)80130-2;
Kaliman A.V., Krutilina A.I., Kryukov V.M., Bayev A.A.;
"Cloning and DNA sequence of the 5'-exonuclease gene of bacteriophage
T5.";
FEBS Lett. 195:61-64(1986).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Ksenzenko V.N., Kaliman A.V., Krutilina A.I., Shlyapnikov M.G.;
"Bacteriophage T5 complete genome.";
Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND INDUCTION.
STRAIN=ATCC 11303-B5 {ECO:0000312|EMBL:AAX12058.1};
PubMed=15661140; DOI=10.1016/j.virol.2004.10.049;
Wang J., Jiang Y., Vincent M., Sun Y., Yu H., Wang J., Bao Q.,
Kong H., Hu S.;
"Complete genome sequence of bacteriophage T5.";
Virology 332:45-65(2005).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=St0 deletion mutant;
PubMed=24198424; DOI=10.1128/JVI.02262-13;
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.;
"Insights into bacteriophage T5 structure from analysis of its
morphogenesis genes and protein components.";
J. Virol. 88:1162-1174(2014).
[5]
PROTEIN SEQUENCE OF 2-20, AND CATALYTIC ACTIVITY.
PubMed=2211703;
Sayers J.R., Eckstein F.;
"Properties of overexpressed phage T5 D15 exonuclease. Similarities
with Escherichia coli DNA polymerase I 5'-3' exonuclease.";
J. Biol. Chem. 265:18311-18317(1990).
[6]
MUTAGENESIS OF ARG-33; ARG-172; LYS-215; ARG-216 AND LYS-241, AND
DNA-BINDING.
PubMed=12084915; DOI=10.1073/pnas.082241699;
Dervan J.J., Feng M., Patel D., Grasby J.A., Artymiuk P.J.,
Ceska T.A., Sayers J.R.;
"Interactions of mutant and wild-type flap endonucleases with
oligonucleotide substrates suggest an alternative model of DNA
binding.";
Proc. Natl. Acad. Sci. U.S.A. 99:8542-8547(2002).
[7]
MUTAGENESIS OF TYR-82.
PubMed=12126622; DOI=10.1016/S0022-2836(02)00547-8;
Patel D., Tock M.R., Frary E., Feng M., Pickering T.J., Grasby J.A.,
Sayers J.R.;
"A conserved tyrosine residue aids ternary complex formation, but not
catalysis, in phage T5 flap endonuclease.";
J. Mol. Biol. 320:1025-1035(2002).
[8]
COFACTOR.
PubMed=12606565; DOI=10.1093/emboj/cdg098;
Tock M.R., Frary E., Sayers J.R., Grasby J.A.;
"Dynamic evidence for metal ion catalysis in the reaction mediated by
a flap endonuclease.";
EMBO J. 22:995-1004(2003).
[9]
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
PubMed=8657312; DOI=10.1038/382090a0;
Ceska T.A., Sayers J.R., Stier G., Suck D.;
"A helical arch allowing single-stranded DNA to thread through T5 5'-
exonuclease.";
Nature 382:90-93(1996).
[10]
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF MUTANT ALA-83,
BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF LYS-83; LYS-196 AND
LYS-215, FUNCTION, AND CATALYTIC ACTIVITY.
PubMed=9874768; DOI=10.1073/pnas.96.1.38;
Garforth S.J., Ceska T.A., Suck D., Sayers J.R.;
"Mutagenesis of conserved lysine residues in bacteriophage T5 5'-3'
exonuclease suggests separate mechanisms of endo- and exonucleolytic
cleavage.";
Proc. Natl. Acad. Sci. U.S.A. 96:38-43(1999).
[11]
X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) OF 2-290, COFACTOR, MUTAGENESIS
OF 128-GLU--ASP-130 AND 201-ASP--ASP-204, AND FUNCTION.
PubMed=15077103; DOI=10.1038/nsmb754;
Feng M., Patel D., Dervan J.J., Ceska T., Suck D., Haq I.,
Sayers J.R.;
"Roles of divalent metal ions in flap endonuclease-substrate
interactions.";
Nat. Struct. Mol. Biol. 11:450-456(2004).
-!- FUNCTION: 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).
{ECO:0000250|UniProtKB:P13319, ECO:0000269|PubMed:15077103,
ECO:0000269|PubMed:9874768}.
-!- CATALYTIC ACTIVITY: Exonucleolytic cleavage in the 5'- to 3'-
direction to yield nucleoside 5'-phosphates.
{ECO:0000269|PubMed:2211703, ECO:0000269|PubMed:9874768}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:12606565,
ECO:0000269|PubMed:15077103};
Note=Divalent metal cations, probably Mg(2+) (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). {ECO:0000269|PubMed:12606565,
ECO:0000269|PubMed:15077103};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
pH dependence:
Optimum pH is 9.3 for the exonuclease activity, 5.5 for
endonuclease activity. {ECO:0000269|PubMed:9874768};
-!- INDUCTION: Expressed in the early phase of the viral replicative
cycle. {ECO:0000305|PubMed:15661140}.
-!- SEQUENCE CAUTION:
Sequence=AAX12058.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AY543070; AAS77176.1; -; Genomic_DNA.
EMBL; AY587007; AAX12058.1; ALT_INIT; Genomic_DNA.
EMBL; AY692264; AAU05267.1; -; Genomic_DNA.
PIR; A23610; NCBPT5.
RefSeq; YP_006958.1; NC_005859.1.
PDB; 1EXN; X-ray; 2.50 A; A/B=2-291.
PDB; 1J5F; Model; -; A=20-289.
PDB; 1UT5; X-ray; 2.75 A; A/B=2-291.
PDB; 1UT8; X-ray; 2.75 A; A/B=2-291.
PDB; 1XO1; X-ray; 2.50 A; A/B=1-291.
PDB; 5HML; X-ray; 1.48 A; A/B=20-291.
PDB; 5HMM; X-ray; 1.50 A; A/B=20-290.
PDB; 5HNK; X-ray; 2.22 A; A/B=20-291.
PDB; 5HP4; X-ray; 1.86 A; A=20-291.
PDBsum; 1EXN; -.
PDBsum; 1J5F; -.
PDBsum; 1UT5; -.
PDBsum; 1UT8; -.
PDBsum; 1XO1; -.
PDBsum; 5HML; -.
PDBsum; 5HMM; -.
PDBsum; 5HNK; -.
PDBsum; 5HP4; -.
ProteinModelPortal; P06229; -.
SMR; P06229; -.
GeneID; 2777611; -.
KEGG; vg:2777611; -.
KO; K18950; -.
OrthoDB; VOG090000FN; -.
EvolutionaryTrace; P06229; -.
Proteomes; UP000002107; Genome.
Proteomes; UP000002141; Genome.
Proteomes; UP000002503; Genome.
GO; GO:0008409; F:5'-3' exonuclease activity; IDA:UniProtKB.
GO; GO:0017108; F:5'-flap endonuclease activity; IDA:UniProtKB.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0033567; P:DNA replication, Okazaki fragment processing; IEA:InterPro.
GO; GO:0039693; P:viral DNA genome replication; IEA:UniProtKB-KW.
InterPro; IPR020046; 5-3_exonucl_a-hlix_arch_N.
InterPro; IPR036279; 5-3_exonuclease_C_sf.
InterPro; IPR002421; 5-3_exonuclease_N.
InterPro; IPR020045; DNA_polI_H3TH.
InterPro; IPR038969; FEN_bact-like.
InterPro; IPR008918; HhH2.
InterPro; IPR029060; PIN-like_dom_sf.
PANTHER; PTHR42646; PTHR42646; 1.
Pfam; PF01367; 5_3_exonuc; 1.
Pfam; PF02739; 5_3_exonuc_N; 1.
SMART; SM00475; 53EXOc; 1.
SMART; SM00279; HhH2; 1.
SUPFAM; SSF47807; SSF47807; 1.
SUPFAM; SSF88723; SSF88723; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Direct protein sequencing;
DNA replication; DNA-binding; Early protein; Endonuclease;
Exonuclease; Hydrolase; Metal-binding; Nuclease; Reference proteome;
Viral DNA replication.
INIT_MET 1 1 Removed; by host.
{ECO:0000269|PubMed:2211703}.
CHAIN 2 291 T5 flap endonuclease.
/FTId=PRO_0000165217.
DOMAIN 190 263 5'-3' exonuclease. {ECO:0000255}.
COMPBIAS 10 15 Poly-Glu. {ECO:0000255}.
ACT_SITE 83 83 Proton acceptor; for exonuclease
activity. {ECO:0000305}.
METAL 26 26 Divalent metal cation 1.
{ECO:0000269|PubMed:15077103,
ECO:0000269|PubMed:8657312}.
METAL 68 68 Divalent metal cation 1.
{ECO:0000269|PubMed:15077103,
ECO:0000269|PubMed:8657312}.
METAL 128 128 Divalent metal cation 1.
{ECO:0000269|PubMed:15077103,
ECO:0000269|PubMed:8657312}.
METAL 131 131 Divalent metal cation 1.
{ECO:0000269|PubMed:15077103,
ECO:0000269|PubMed:8657312}.
METAL 153 153 Divalent metal cation 1.
{ECO:0000269|PubMed:15077103,
ECO:0000269|PubMed:8657312}.
METAL 153 153 Divalent metal cation 2.
{ECO:0000269|PubMed:15077103,
ECO:0000269|PubMed:8657312}.
METAL 155 155 Divalent metal cation 2.
{ECO:0000269|PubMed:15077103,
ECO:0000269|PubMed:8657312}.
METAL 201 201 Divalent metal cation 2.
{ECO:0000269|PubMed:15077103,
ECO:0000269|PubMed:8657312}.
METAL 204 204 Divalent metal cation 2.
{ECO:0000269|PubMed:15077103,
ECO:0000269|PubMed:8657312}.
MUTAGEN 33 33 R->A: 10 fold increase in the
dissociation constant for pseudo-Y
binding. 3 fold increase in the
dissociation constant for 5'overhangs
binding. {ECO:0000269|PubMed:12084915}.
MUTAGEN 82 82 Y->F: 3.5-fold decrease in binding
affinity for DNA. No effect on
endonuclease and exonuclease activities.
{ECO:0000269|PubMed:12126622}.
MUTAGEN 83 83 K->A: No exonuclease activity, retains
full endonuclease activity on a flap
structure. Binds DNA pseudo-Y substrates
with a dissociation constant of 200 nM.
{ECO:0000269|PubMed:9874768}.
MUTAGEN 128 130 EAD->QAN: Loss of both exo- and
endonuclease activity, still binds DNA.
{ECO:0000269|PubMed:15077103}.
MUTAGEN 172 172 R->A: 10 fold increase in the
dissociation constant for pseudo-Y
binding. No effect on 5'overhangs
binding. {ECO:0000269|PubMed:12084915}.
MUTAGEN 196 196 K->A: 10% exonuclease activity, little
change in endonuclease activity. Binds
DNA pseudo-Y substrates with a
dissociation constant of 200 nM.
{ECO:0000269|PubMed:9874768}.
MUTAGEN 201 204 DLGD->ILGS: Retains most endo- but very
little exonuclease activity; binds
pseudo-Y substrate more tightly than wt.
{ECO:0000269|PubMed:15077103}.
MUTAGEN 201 204 DLGD->RLGP,RLGR: Retains most
endonuclease but complete loss of
exonuclease activity; binds pseudo-Y
substrate more tightly than wt.
{ECO:0000269|PubMed:15077103}.
MUTAGEN 215 215 K->A: 10 fold increase in the
dissociation constant for pseudo-Y
binding. Drastic increase in the
dissociation constant for 5'overhangs
binding. {ECO:0000269|PubMed:12084915}.
MUTAGEN 215 215 K->A: Wild-type exo- and endonuclease
activities. Binds DNA pseudo-Y substrates
with a dissociation constant of 50 nM.
{ECO:0000269|PubMed:9874768}.
MUTAGEN 216 216 R->A: 100 fold increase in the
dissociation constant for pseudo-Y
binding. Drastic increase in the
dissociation constant for 5'overhangs
binding. {ECO:0000269|PubMed:12084915}.
MUTAGEN 241 241 K->A: 10 fold increase in the
dissociation constant for pseudo-Y
binding. 10 fold increase in the
dissociation constant for 5'overhangs
binding. {ECO:0000269|PubMed:12084915}.
STRAND 21 26 {ECO:0000244|PDB:5HML}.
HELIX 27 31 {ECO:0000244|PDB:5HML}.
HELIX 32 34 {ECO:0000244|PDB:5HML}.
HELIX 35 40 {ECO:0000244|PDB:5HML}.
HELIX 44 57 {ECO:0000244|PDB:5HML}.
STRAND 60 66 {ECO:0000244|PDB:5HML}.
HELIX 73 78 {ECO:0000244|PDB:5HML}.
TURN 80 83 {ECO:0000244|PDB:5HML}.
HELIX 84 91 {ECO:0000244|PDB:5HML}.
HELIX 95 118 {ECO:0000244|PDB:5HML}.
HELIX 129 140 {ECO:0000244|PDB:5HML}.
HELIX 141 143 {ECO:0000244|PDB:5HML}.
STRAND 147 150 {ECO:0000244|PDB:5HML}.
HELIX 154 159 {ECO:0000244|PDB:5HML}.
STRAND 164 167 {ECO:0000244|PDB:5HML}.
TURN 169 171 {ECO:0000244|PDB:5HML}.
STRAND 173 175 {ECO:0000244|PDB:1EXN}.
HELIX 177 179 {ECO:0000244|PDB:5HML}.
HELIX 180 184 {ECO:0000244|PDB:5HML}.
STRAND 185 188 {ECO:0000244|PDB:5HML}.
HELIX 189 199 {ECO:0000244|PDB:5HML}.
HELIX 202 204 {ECO:0000244|PDB:5HML}.
HELIX 214 224 {ECO:0000244|PDB:5HML}.
HELIX 227 233 {ECO:0000244|PDB:5HML}.
HELIX 241 247 {ECO:0000244|PDB:5HML}.
HELIX 250 260 {ECO:0000244|PDB:5HML}.
HELIX 262 271 {ECO:0000244|PDB:5HML}.
HELIX 275 289 {ECO:0000244|PDB:5HML}.
SEQUENCE 291 AA; 33448 MW; 234C9564E491B4E9 CRC64;
MSKSWGKFIE EEEAEMASRR NLMIVDGTNL GFRFKHNNSK KPFASSYVST IQSLAKSYSA
RTTIVLGDKG KSVFRLEHLP EYKGNRDEKY AQRTEEEKAL DEQFFEYLKD AFELCKTTFP
TFTIRGVEAD DMAAYIVKLI GHLYDHVWLI STDGDWDTLL TDKVSRFSFT TRREYHLRDM
YEHHNVDDVE QFISLKAIMG DLGDNIRGVE GIGAKRGYNI IREFGNVLDI IDQLPLPGKQ
KYIQNLNASE ELLFRNLILV DLPTYCVDAI AAVGQDVLDK FTKDILEIAE Q


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