P0AB83 (END3_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Endonuclease III
EC=4.2.99.18

Alternative name(s):
DNA-(apurinic or apyrimidinic site) lyase

Gene names

Name:	nth
Ordered Locus Names:	b1633, JW1625

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	211 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N-glycosidic bond, leaving an AP (apurinic/apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. Ref.1 Ref.5 Ref.6
Catalytic activity	The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. Ref.6
Cofactor	Binds 1 4Fe-4S cluster. The cluster is not important for the catalytic activity, but is probably involved in DNA-binding and proper positioning of the enzyme along the DNA strand. Ref.7 Ref.9
Subunit structure	Monomer. Ref.5
Sequence similarities	Belongs to the Nth/MutY family. Contains 1 HhH domain.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Ligand	4Fe-4S DNA-binding Iron Iron-sulfur Metal-binding
Molecular function	Glycosidase Hydrolase Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	base-excision repair Inferred from electronic annotation. Source: InterPro
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: UniProtKB-KW DNA-(apurinic or apyrimidinic site) lyase activity Inferred from electronic annotation. Source: EC endonuclease activity Inferred from electronic annotation. Source: InterPro hydrolase activity, acting on glycosyl bonds Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
aceE	P0AFG8	2	EBI-555213,EBI-542683

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 211

211

Endonuclease III HAMAP-Rule MF_00942

PRO_0000102210

Regions

Domain

108 – 127

20

HhH

Sites

Metal binding

187

1

Iron-sulfur (4Fe-4S)

Metal binding

194

1

Iron-sulfur (4Fe-4S)

Metal binding

197

1

Iron-sulfur (4Fe-4S)

Metal binding

203

1

Iron-sulfur (4Fe-4S)

Experimental info

Mutagenesis

120

1

K → Q: 100000-fold decrease in activity and slight decrease in substrate affinity. Ref.9

Mutagenesis

138

1

D → N: 100-fold decrease in activity and 4-fold increase in substrate affinity. Ref.9

Mutagenesis

191

1

K → E: Slight decrease in activity and 130-fold increase in substrate affinity. Ref.9

Secondary structure

1

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211

Helix Strand Turn

Details...

Helix

3 – 16

14

Helix

29 – 38

10

Turn

39 – 41

3

Helix

44 – 54

11

Turn

55 – 57

3

Helix

61 – 76

16

Helix

82 – 98

17

Turn

99 – 102

4

Helix

108 – 113

6

Helix

119 – 130

12

Helix

139 – 148

10

Helix

156 – 166

11

Helix

169 – 171

3

Turn

172 – 174

3

Helix

175 – 185

11

Beta strand

189 – 191

3

Helix

194 – 196

3

Helix

200 – 202

3

Sequences

	Sequence		Length	Mass (Da)
	P0AB83 [UniParc]. Last modified November 8, 2005. Version 1. Checksum: FF4245823B7F902B	FASTA	211	23,562
	10 20 30 40 50 60 MNKAKRLEIL TRLRENNPHP TTELNFSSPF ELLIAVLLSA QATDVSVNKA TAKLYPVANT 70 80 90 100 110 120 PAAMLELGVE GVKTYIKTIG LYNSKAENII KTCRILLEQH NGEVPEDRAA LEALPGVGRK 130 140 150 160 170 180 TANVVLNTAF GWPTIAVDTH IFRVCNRTQF APGKNVEQVE EKLLKVVPAE FKVDCHHWLI 190 200 210 LHGRYTCIAR KPRCGSCIIE DLCEYKEKVD I

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Purification and characterization of Escherichia coli endonuclease III from the cloned nth gene." Asahara H., Wistort P.M., Bank J.F., Bakerian R.H., Cunningham R.P. Biochemistry 28:4444-4449(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10, FUNCTION.
[2]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"DNA glycosylase activities for thymine residues damaged by ring saturation, fragmentation, or ring contraction are functions of endonuclease III in Escherichia coli." Breimer L.H., Lindahl T. J. Biol. Chem. 259:5543-5548(1984) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBUNIT.
[6]	"The mechanisms of action of E. coli endonuclease III and T4 UV endonuclease (endonuclease V) at AP sites." Kim J., Linn S. Nucleic Acids Res. 16:1135-1141(1988) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY.
[7]	"Structure and function of Escherichia coli endonuclease III." Cunningham R.P., Ahern H., Xing D., Thayer M.M., Tainer J.A. Ann. N. Y. Acad. Sci. 726:215-222(1994) [PubMed] [Europe PMC] [Abstract] Cited for: COFACTOR.
[8]	"Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III." Kuo C.-F., McRee D., Fisher C.L., O'Handley S.F., Cunningham R.P., Tainer J.A. Science 258:434-440(1992) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
[9]	"Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure." Thayer M.M., Ahern H., Xing D., Cunningham R.P., Tainer J.A. EMBO J. 14:4108-4120(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), COFACTOR, DNA-BINDING, MUTAGENESIS OF LYS-120; ASP-138 AND LYS-191.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J02857 Genomic DNA. Translation: AAA24227.1.
U00096 Genomic DNA. Translation: AAC74705.1.
AP009048 Genomic DNA. Translation: BAA15387.1.

PIR

A32412.

RefSeq

NP_416150.1. NC_000913.2.
YP_489897.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2ABK	X-ray	1.85	A	1-211	[»]

ProteinModelPortal

P0AB83.

SMR

P0AB83. Positions 1-211.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-48071N.

IntAct

P0AB83. 6 interactions.

MINT

MINT-1223379.

STRING

511145.b1633.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC74705; AAC74705; b1633.
BAA15387; BAA15387; BAA15387.

GeneID

12933192.
947122.

KEGG

ecj:Y75_p1610.
eco:b1633.

PATRIC

32118568. VBIEscCol129921_1704.

Organism-specific databases

EchoBASE

EB0656.

EcoGene

EG10662. nth.

Phylogenomic databases

eggNOG

COG0177.

HOGENOM

HOG000252206.

KO

K10773.

OMA

NNKSKHL.

ProtClustDB

PRK10702.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10662-MONOMER.
ECOL316407:JW1625-MONOMER.

Gene expression databases

Genevestigator

P0AB83.

Family and domain databases

Gene3D

1.10.1670.10. 1 hit.
1.10.340.30. 1 hit.

HAMAP

MF_00942. Nth.

InterPro

IPR011257. DNA_glycosylase.
IPR004036. Endonuclease-III_CS2.
IPR005759. Endonuclease-III_Nth.
IPR004035. Endouclease-III_FeS-bd_BS.
IPR003651. Endouclease3_FeS-loop_motif.
IPR003265. HhH-GPD_domain.
IPR000445. HhH_motif.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR023170. HTH_base_excis_C.
[Graphical view]

Pfam

PF10576. EndIII_4Fe-2S. 1 hit.
PF00633. HHH. 1 hit.
PF00730. HhH-GPD. 1 hit.
[Graphical view]

PIRSF

PIRSF001435. Nth. 1 hit.

SMART

SM00478. ENDO3c. 1 hit.
SM00525. FES. 1 hit.
SM00278. HhH1. 1 hit.
[Graphical view]

SUPFAM

SSF48150. DNA_glycsylse. 1 hit.

TIGRFAMs

TIGR01083. nth. 1 hit.

PROSITE

PS00764. ENDONUCLEASE_III_1. 1 hit.
PS01155. ENDONUCLEASE_III_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0AB83.

Entry information

Entry name

END3_ECOLI

Accession

Primary (citable) accession number: P0AB83
Secondary accession number(s): P20625

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 8, 2005
Last sequence update:	November 8, 2005
Last modified:	May 1, 2013
This is version 76 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program