Reviewed, UniProtKB/Swiss-Prot P0AB83 (END3_ECOLI)

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) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	211 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Has both an apurinic and/or apyrimidinic endonuclease activity and a DNA N-glycosylase activity. Incises damaged DNA at cytosines, thymines and guanines. Acts on a damaged strand, 5' from the damaged site. Required for the repair of both oxidative DNA damage and spontaneous mutagenic lesions.
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.
Cofactor	Binds 1 4Fe-4S cluster. The cluster is not important for the catalytic activity, but which is probably involved in the proper positioning of the enzyme along the DNA strand.
Subunit structure	Monomer.
Sequence similarities	Belongs to the nth/mutY family.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding
Molecular function	Glycosidase Hydrolase Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	base-excision repair Inferred from electronic annotation. Source: InterPro
Cellular component	intracellular 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: InterPro 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 iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
aceE	P0AFG8	1	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

PRO_0000102210

Sites

Active site

112

1

Nucleophile; for N-glycosylase activity Probable

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: 10000-fold decrease in activity. Ref.5

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

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)
	P0AB83-1 [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: 2669955] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10.
[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: 9097039] [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: 9278503] [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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"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: 8092678] [Abstract] Cited for: MUTAGENESIS OF LYS-120.
[6]	"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: 1411536] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
[7]	"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: 7664751] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).

Cross-references

Sequence databases

EMBLGenBankDDBJ

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

PIR

A32412.

RefSeq

AP_002255.1.
NP_416150.1.

3D structure databases

PDBPDBe

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

ModBase

Search...

Protein-protein interaction databases

IntAct

P0AB83. 6 interactions.

Genome annotation databases

GeneID

947122.

GenomeReviews

Gene locus JW1625 in contig AP009048_GR.
Gene locus b1633 in contig U00096_GR.

KEGG

ecj:JW1625.
eco:b1633.

Organism-specific databases

EchoBASE

EB0656.

EcoGene

EG10662. nth.

CMR

Search...

Phylogenomic databases

HOGENOM

P0AB83.

OMA

P0AB83. EPTIAVD.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10662-MON.

Family and domain databases

InterPro

IPR004036. Endonuclease-III_CS2.
IPR005759. Endonuclease-III_Nth.
IPR004035. Endouclease-III_FeS-bd_CS1.
IPR003651. Endouclease3-like_FeS-loop.
IPR003583. Helix-hairpin-helix_DNA-bd.
IPR003265. HhH-GPD_domain.
IPR000445. HhH_motif.
[Graphical view]

Pfam

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

SMART

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

TIGRFAMs

TIGR01083. nth. 1 hit.

PROSITE

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

ProtoNet

Search...

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:	June 16, 2009
This is version 40 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)