{PDOC00599}
{PS00729; AP_NUCLEASE_F2_1}
{PS00730; AP_NUCLEASE_F2_2}
{PS00731; AP_NUCLEASE_F2_3}
{PS51432; AP_NUCLEASE_F2_4}
{BEGIN}
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* AP endonucleases family 2 signatures and profile *
****************************************************

Cellular  DNA  is  spontaneously and continuously damaged by environmental and
internal  factors  such  as  X-rays, UV light and agents such as the antitumor
drugs  bleomycin  and neocarzinostatin or those that generate oxygen radicals.
Apurinic/apyrimidinic  (AP)  sites  form  both  spontaneously  and  as  highly
cytotoxic  intermediates  in  the  removal  of  the  damaged  base by the base
excision  repair  (BER)  pathway.  DNA  repair at the AP sites is initiated by
specific   endonuclease   cleavage   of   the  phosphodiester  backbone.  Such
endonucleases  are also generally capable of removing blocking groups from the
3'terminus of DNA strand breaks.

AP  endonucleases can be classified into two families on the basis of sequence
similarity  and  structure  (cf.  family 1 <PDOC00598>). What we call family 2
groups the enzymes listed below [1,2].

 - Bacterial endonuclease IV (gene nfo) (EC 3.1.21.2).
 - Fungal and Caenorhabditis elegans apurinic endonuclase APN1 (EC 4.2.99.18).
 - Dictyostelium endonuclease 4 homolog (EC 3.1.21.2).
 - Archaeal probable endonuclease 4 homologs (EC 3.1.21.2). 
 - Mimivirus putative endonuclease 4 (EC 3.1.21.2).

APN1  and nfo have been shown to be transition metalloproteins that bind three
zinc  ions  [3,4].  The  metal-binding sites have been determined from the 3D-
structure  of  Escherichia  coli nfo [4,6,7], which shows an alpha/beta-barrel
fold (see <PDB:1QTW; A>) similar to that of other divalent metal-dependent TIM
barrel enzymes (see <PDOC00155>), such as xylose isomerase (see <PDOC00156>).

We developed three signature patterns for this family of enzymes. The patterns
are based on regions that contain conserved residues involved in zinc-binding.
We  also  developed  a profile that covers the entire AP endonuclease family 2
structure.

-Consensus pattern: H-[GSAD]-x-Y-[LIF]-[LIMN]-N-[LIVMFCAP]-[AGC]
                    [The H is a zinc ligand]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Consensus pattern: [GSARY]-[LIVMF]-[CT]-[LIVMFY]-D-T-C-H
                    [The D and the H are zinc ligands]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Consensus pattern: [LIVMFW]-H-x-N-[DEG]-[SA]-x(4)-[GNAQ]-x(3)-D-x-H
                    [The 2 H's and the D are zinc ligands]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Last update: February 2009 / Text revised; profile added.

[ 1] Popoff S.C., Spira A.I., Johnson A.W., Demple B.
     "Yeast structural gene (APN1) for the major apurinic endonuclease:
     homology to Escherichia coli endonuclease IV."
     Proc. Natl. Acad. Sci. U.S.A. 87:4193-4197(1990).
     PubMed=1693433
[ 2] Barzilay G., Hickson I.D.
     "Structure and function of apurinic/apyrimidinic endonucleases."
     BioEssays 17:713-719(1995).
     PubMed=7661852
[ 3] Levin J.D., Shapiro R., Demple B.
     "Metalloenzymes in DNA repair. Escherichia coli endonuclease IV and
     Saccharomyces cerevisiae Apn1."
     J. Biol. Chem. 266:22893-22898(1991).
     PubMed=1720775
[ 4] Hosfield D.J., Guan Y., Haas B.J., Cunningham R.P., Tainer J.A.
     "Structure of the DNA repair enzyme endonuclease IV and its DNA
     complex: double-nucleotide flipping at abasic sites and
     three-metal-ion catalysis."
     Cell 98:397-408(1999).
     PubMed=10458614
[ 5] Ishchenko A.A., Sanz G., Privezentzev C.V., Maksimenko A.V.,
     Saparbaev M.
     "Characterisation of new substrate specificities of Escherichia coli
     and Saccharomyces cerevisiae AP endonucleases."
     Nucleic Acids Res. 31:6344-6353(2003).
     PubMed=14576322
[ 6] Ivanov I., Tainer J.A., McCammon J.A.
     "Unraveling the three-metal-ion catalytic mechanism of the DNA repair
     enzyme endonuclease IV."
     Proc. Natl. Acad. Sci. U.S.A. 104:1465-1470(2007).
     PubMed=17242363; DOI=10.1073/pnas.0603468104
[ 7] Garcin E.D., Hosfield D.J., Desai S.A., Haas B.J., Bjoras M.,
     Cunningham R.P., Tainer J.A.
     "DNA apurinic-apyrimidinic site binding and excision by endonuclease
     IV."
     Nat. Struct. Mol. Biol. 15:515-522(2008).
     PubMed=18408731; DOI=10.1038/nsmb.1414
{END}