P06229 (EXO5_BPT5) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Exodeoxyribonuclease
EC=3.1.11.3

Alternative name(s):
5'-exonuclease
T5FEN

Gene names

Name:

D15

Organism

Enterobacteria phage T5 (Bacteriophage T5) [Reference proteome]

Taxonomic identifier

10726 [NCBI]

Taxonomic lineage

Viruses › dsDNA viruses, no RNA stage › Caudovirales › Siphoviridae › T5likevirus

Virus host

Escherichia coli [TaxID: 562]

Protein attributes

Sequence length	291 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 activity	Exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates.
Cofactor	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. Ref.5
Sequence similarities	Contains 1 5'-3' exonuclease domain.
Biophysicochemical properties	pH dependence: Optimum pH is 9.3 for the exonuclease activity, 5.5 for endonuclease activity. Ref.4

Ontologies

Keywords
Ligand	DNA-binding Metal-binding
Molecular function	Endonuclease Exonuclease Hydrolase Nuclease
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC
Molecular_function	5'-3' exonuclease activity Inferred from electronic annotation. Source: InterPro DNA binding Inferred from electronic annotation. Source: UniProtKB-KW endonuclease activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed; by host

Chain

2 – 291

290

Exodeoxyribonuclease

PRO_0000165217

Sites

Active site

83

1

Proton acceptor (Probable); for exonuclease activity

Metal binding

26

1

Divalent metal cation 1 Probable

Metal binding

68

1

Divalent metal cation 1 Probable

Metal binding

128

1

Divalent metal cation 1 Probable

Metal binding

131

1

Divalent metal cation 1 Probable

Metal binding

153

1

Divalent metal cation 1 Probable

Metal binding

153

1

Divalent metal cation 2 Probable

Metal binding

155

1

Divalent metal cation 2 Probable

Metal binding

201

1

Divalent metal cation 2 Probable

Metal binding

204

1

Divalent metal cation 2 Probable

Experimental info

Mutagenesis

83

1

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. Ref.4

Mutagenesis

128 – 130

3

EAD → QAN: Loss of both exo- and endonuclease activity, still binds DNA. Ref.5

Mutagenesis

196

1

K → A: 10% exonuclease activity, little change in endonuclease activity. Binds DNA pseudo-Y substrates with a dissociation constant of 200 nM. Ref.4

Mutagenesis

201 – 204

4

DLGD → ILGS: Retains most endo- but very little exonuclease activity; binds pseudo-Y substrate more tightly than wt. Ref.5

Mutagenesis

201 – 204

4

DLGD → RLGP or RLGR: Retains most endonuclease but complete loss of exonuclease activity; binds pseudo-Y substrate more tightly than wt. Ref.5

Mutagenesis

215

1

K → A: Wild-type exo- and endonuclease activities. Binds DNA pseudo-Y substrates with a dissociation constant of 50 nM. Ref.4

Secondary structure

1

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291

Helix Strand Turn

Details...

Beta strand

21 – 26

6

Helix

27 – 37

11

Beta strand

39 – 41

3

Helix

44 – 57

14

Beta strand

60 – 66

7

Helix

73 – 78

6

Turn

80 – 83

4

Helix

84 – 91

8

Helix

95 – 115

21

Turn

116 – 118

3

Helix

129 – 140

12

Helix

141 – 143

3

Beta strand

147 – 150

4

Helix

154 – 159

6

Beta strand

162 – 168

7

Turn

169 – 172

4

Beta strand

173 – 175

3

Helix

177 – 179

3

Helix

180 – 184

5

Beta strand

185 – 188

4

Helix

189 – 199

11

Helix

202 – 204

3

Helix

214 – 224

11

Helix

227 – 233

7

Helix

241 – 247

7

Helix

250 – 260

11

Helix

262 – 271

10

Helix

275 – 288

14

Sequences

	Sequence		Length	Mass (Da)
	P06229 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 234C9564E491B4E9	FASTA	291	33,448
	10 20 30 40 50 60 MSKSWGKFIE EEEAEMASRR NLMIVDGTNL GFRFKHNNSK KPFASSYVST IQSLAKSYSA 70 80 90 100 110 120 RTTIVLGDKG KSVFRLEHLP EYKGNRDEKY AQRTEEEKAL DEQFFEYLKD AFELCKTTFP 130 140 150 160 170 180 TFTIRGVEAD DMAAYIVKLI GHLYDHVWLI STDGDWDTLL TDKVSRFSFT TRREYHLRDM 190 200 210 220 230 240 YEHHNVDDVE QFISLKAIMG DLGDNIRGVE GIGAKRGYNI IREFGNVLDI IDQLPLPGKQ 250 260 270 280 290 KYIQNLNASE ELLFRNLILV DLPTYCVDAI AAVGQDVLDK FTKDILEIAE Q

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AY543070 Genomic DNA. Translation: AAS77176.1.

PIR

NCBPT5. A23610.

RefSeq

YP_006958.1. NC_005859.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	2-290	[»]
1UT8	X-ray	2.75	A/B	2-290	[»]
1XO1	X-ray	2.50	A/B	1-291	[»]

ProteinModelPortal

P06229.

SMR

P06229. Positions 20-291.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

2777611.

Phylogenomic databases

ProtClustDB

CLSP2493332.

Family and domain databases

InterPro

IPR020046. 5-3_exonucl_a-hlix_arch_N.
IPR020045. 5-3_exonuclease_C.
IPR002421. 5-3_exonuclease_N.
IPR008918. HhH2.
[Graphical view]

Pfam

PF01367. 5_3_exonuc. 1 hit.
PF02739. 5_3_exonuc_N. 1 hit.
[Graphical view]

SMART

SM00475. 53EXOc. 1 hit.
SM00279. HhH2. 1 hit.
[Graphical view]

SUPFAM

SSF47807. 5_3_exo_C. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P06229.

Entry information

Entry name

EXO5_BPT5

Accession

Primary (citable) accession number: P06229

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1988
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 94 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program