PROSITE documentation PDOC00615

Endonuclease III signatures

Description

Escherichia coli endonuclease III (EC 4.2.99.18) (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)
Consensus pattern: C-x(3)-[KRSN]-P-[KRAGL]-C-x(2)-C-x(5)-C
The 4 C's are 4Fe-4S ligands
Sequences known to belong to this class detected by the pattern: ALL, except for nth1 and MJ0613
Other sequence(s) detected in Swiss-Prot: NONE.
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS00764
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS00764
• Scan Swiss-Prot/TrEMBL entries against PS00764
• view ligand binding statistics
Matching PDB structures: 1KEA 1KG2 1KG3 1KG4 ... [ALL]
ENDONUCLEASE_III_2, PS01155; Endonuclease III family signature  (PATTERN)
Consensus pattern: [GSTENA]-x-[LIVMF]-P-x(5)-[LIVMW]-x(2,3)-[LI]-[PAS]-G-[IV]-[GA]-x(3)-[GAC]-x(2,3)-[LIVMA]-x(1,2)-[GSALVI]-[LIVMFYW]-[GANKD]
Sequences known to belong to this class detected by the pattern: ALL
Other sequence(s) detected in Swiss-Prot: NONE.
• Retrieve an alignment of Swiss-Prot true positive hits:
  Clustal format, color, condensed view  / Clustal format, color  / Clustal format, plain text  / Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic tree view of all Swiss-Prot/TrEMBL entries matching PS01155
• Retrieve a list of all Swiss-Prot/TrEMBL entries matching PS01155
• Scan Swiss-Prot/TrEMBL entries against PS01155
• view ligand binding statistics
Matching PDB structures: 1KEA 1KG2 1KG3 1KG4 ... [ALL]

References

1 Authors Kuo C.-F., McRee D.E., Fisher C.L., O'Handley S.F., Cunningham R.P., Tainer J.A.
Title Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III.
Source Science 258:434-440(1992).
PubMed ID 1411536
2 Authors Thomson A.J.
Title Crosslinked by a cluster.
Source Curr. Biol. 3:173-174(1993).
PubMed ID 15335790
3 Authors Roldan-Arjona T., Anselmino C., Lindahl T.
Source Nucleic Acids Res. 24:3307-3312(1996).
4 Authors Noelling J., van Eeden F.J.M., Eggen R.I.L., de Vos W.M.
Source Nucleic Acids Res. 20:6501-6507(1992).

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