Due to scheduled maintenance work, this service may not be available on Monday January 22nd between 08.00 am and 9.00 am CEST.
To improve security and privacy, we are moving our web pages and services from HTTP to HTTPS.
To give users of web services time to transition to HTTPS, we will support separate HTTP and HTTPS services until the end of 2017.
From January 2018 most HTTP traffic will be automatically redirected to HTTPS. [more...]
View this page in https
PROSITE documentation PDOC00615

Endonuclease III signatures


Escherichia coli endonuclease III (EC (gene nth) [1] is a DNA repair enzyme that acts both as a DNA N-glycosylase, removing oxidized pyrimidines from DNA, and as an apurinic/apyrimidinic (AP) endonuclease, introducing a single-strand nick at the site from which the damaged base was removed. Endonuclease III is an iron-sulfur protein that binds a single 4Fe-4S cluster. The 4Fe-4S cluster does not seem to be important for catalytic activity, but is probably involved in the proper positioning of the enzyme along the DNA strand [2].

Endonuclease III is evolutionary related to the following proteins:

  • Fission yeast endonuclease III homolog (gene nth1) [3].
  • Escherichia coli and related protein DNA repair protein mutY, which is an adenine glycosylase. MutY is a larger protein (350 amino acids) than endonuclease III (211 amino acids).
  • Micrococcus luteus ultraviolet N-glycosylase/AP lyase which initiates repair at cis-syn pyrimidine dimers.
  • ORF10 in plasmid pFV1 of the thermophilic archaebacteria Methanobacterium thermoformicicum [4]. Restriction methylase m.MthTI, which is encoded by this plasmid, generates 5-methylcytosine which is subject to deamination resulting in G-T mismatches. This protein could correct these mismatches.
  • Yeast hypothetical protein YAL015c.
  • Fission yeast hypothetical protein SpAC26A3.02.
  • Caenorhabditis elegans hypothetical protein R10E4.5.
  • Methanococcus jannaschii hypothetical protein MJ0613.

The 4Fe-4S cluster is bound by four cysteines which are all located in a 17 amino acid region at the C-terminal end of endonuclease III. A similar region is also present in the central section of mutY and in the C-terminus of ORF10 and of the Micrococcus UV endonuclease. The 4Fe-4S cluster region does not exist in YAL015c.

We developed two signature patterns for these proteins: the first corresponds to the core of the iron-sulfur binding domain, the second corresponds to the best conserved region in the catalytic core of these enzymes.

Last update:

December 2004 / Pattern and text revised.

Technical section

PROSITE methods (with tools and information) covered by this documentation:

ENDONUCLEASE_III_1, PS00764; Endonuclease III iron-sulfur binding region signature  (PATTERN)

ENDONUCLEASE_III_2, PS01155; Endonuclease III family signature  (PATTERN)


1AuthorsKuo C.-F., McRee D.E., Fisher C.L., O'Handley S.F., Cunningham R.P., Tainer J.A.
TitleAtomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III.
SourceScience 258:434-440(1992).
PubMed ID1411536

2AuthorsThomson A.J.
TitleCrosslinked by a cluster.
SourceCurr. Biol. 3:173-174(1993).
PubMed ID15335790

3AuthorsRoldan-Arjona T., Anselmino C., Lindahl T.
SourceNucleic Acids Res. 24:3307-3312(1996).

4AuthorsNoelling J., van Eeden F.J.M., Eggen R.I.L., de Vos W.M.
SourceNucleic Acids Res. 20:6501-6507(1992).

PROSITE is copyright. It is produced by the SIB Swiss Institute Bioinformatics. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Usage by and for commercial entities requires a license agreement. For information about the licensing scheme send an email to
Prosite License or see: prosite_license.html.


View entry in original PROSITE document format
View entry in raw text format (no links)