APE_ASFP4
ID APE_ASFP4 Reviewed; 296 AA.
AC P0C9C6;
DT 05-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 05-MAY-2009, sequence version 1.
DT 03-AUG-2022, entry version 50.
DE RecName: Full=Probable AP endonuclease {ECO:0000250|UniProtKB:Q65202};
DE Short=APE {ECO:0000250|UniProtKB:Q65202};
DE EC=3.1.21.- {ECO:0000250|UniProtKB:Q65202};
GN OrderedLocusNames=Pret-146;
OS African swine fever virus (isolate Tick/South Africa/Pretoriuskop Pr4/1996)
OS (ASFV).
OC Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota; Pokkesviricetes;
OC Asfuvirales; Asfarviridae; Asfivirus.
OX NCBI_TaxID=561443;
OH NCBI_TaxID=6937; Ornithodoros (relapsing fever ticks).
OH NCBI_TaxID=85517; Phacochoerus aethiopicus (Warthog).
OH NCBI_TaxID=41426; Phacochoerus africanus (Warthog).
OH NCBI_TaxID=273792; Potamochoerus larvatus (Bushpig).
OH NCBI_TaxID=9823; Sus scrofa (Pig).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Kutish G.F., Rock D.L.;
RT "African swine fever virus genomes.";
RL Submitted (MAR-2003) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS), DNA-BINDING, DISULFIDE BOND,
RP BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND MUTAGENESIS OF CYS-16 AND
RP CYS-20.
RX PubMed=32194979; DOI=10.1038/s41421-020-0146-2;
RA Chen Y., Chen X., Huang Q., Shao Z., Gao Y., Li Y., Yang C., Liu H., Li J.,
RA Wang Q., Ma J., Zhang Y.Z., Gu Y., Gan J.;
RT "A unique DNA-binding mode of African swine fever virus AP endonuclease.";
RL Cell Discov. 6:13-13(2020).
CC -!- FUNCTION: Endonuclease that plays a role in DNA repair (By similarity).
CC Cleaves phosphodiester bonds on the 5' side of apurinic or apyrimidinic
CC sites (AP sites) (By similarity). In addition to endonuclease activity,
CC the ASFV enzyme has a proofreading 3'-5' exonuclease activity that is
CC considerably more efficient in the elimination of a mismatch than in
CC that of a correctly paired base (By similarity). Displays 3'-
CC phosphatase and 3'-repair diesterase activities (By similarity). The
CC single nucleotide gaps generated by the AP endonuclease are filled by
CC the viral AP endonuclease and DNA ligase (Probable).
CC {ECO:0000250|UniProtKB:Q65202, ECO:0000305}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00763,
CC ECO:0000269|PubMed:32194979};
CC Note=Binds 3 Zn(2+) ions. {ECO:0000269|PubMed:32194979};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6.3. {ECO:0000269|PubMed:32194979};
CC -!- SUBCELLULAR LOCATION: Host nucleus {ECO:0000250|UniProtKB:Q65202}. Host
CC cytoplasm {ECO:0000250|UniProtKB:Q65202}. Virion
CC {ECO:0000250|UniProtKB:Q65202}. Note=The early enzyme is localized in
CC the nucleus and the cytoplasm, while the late protein is found only in
CC the cytoplasm (By similarity). Found in association with viral nucleoid
CC (By similarity). {ECO:0000250|UniProtKB:Q65202}.
CC -!- INDUCTION: Expressed in the early phase of the viral replicative cycle
CC and accumulates at later times. {ECO:0000305}.
CC -!- MISCELLANEOUS: Consistent with its intracellular location, ASFV encodes
CC its own replicative DNA polymerase and three base excision repair
CC enzymes: a class II AP endonuclease, the repair polymerase Pol X, and
CC an ATP-dependent DNA ligase. {ECO:0000250}.
CC -!- MISCELLANEOUS: During infection, the protein is expressed at early
CC times and accumulates at later times. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the AP endonuclease 2 family.
CC {ECO:0000255|PROSITE-ProRule:PRU00763}.
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DR EMBL; AY261363; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PDB; 6KHY; X-ray; 3.01 A; A/B/C/D=1-296.
DR PDB; 6KI3; X-ray; 2.35 A; A/B=1-296.
DR PDBsum; 6KHY; -.
DR PDBsum; 6KI3; -.
DR SMR; P0C9C6; -.
DR Proteomes; UP000000859; Genome.
DR GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR CDD; cd00019; AP2Ec; 1.
DR InterPro; IPR001719; AP_endonuc_2.
DR InterPro; IPR018246; AP_endonuc_F2_Zn_BS.
DR InterPro; IPR036237; Xyl_isomerase-like_sf.
DR InterPro; IPR013022; Xyl_isomerase-like_TIM-brl.
DR PANTHER; PTHR21445; PTHR21445; 1.
DR Pfam; PF01261; AP_endonuc_2; 1.
DR SMART; SM00518; AP2Ec; 1.
DR SUPFAM; SSF51658; SSF51658; 1.
DR PROSITE; PS00731; AP_NUCLEASE_F2_3; 1.
DR PROSITE; PS51432; AP_NUCLEASE_F2_4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; DNA damage; DNA repair; Early protein;
KW Endonuclease; Exonuclease; Host cytoplasm; Host nucleus; Hydrolase;
KW Metal-binding; Nuclease; Virion; Zinc.
FT CHAIN 1..296
FT /note="Probable AP endonuclease"
FT /id="PRO_0000373139"
FT BINDING 78
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:32194979"
FT BINDING 115
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:32194979"
FT BINDING 142
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00763,
FT ECO:0000269|PubMed:32194979"
FT BINDING 182
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00763,
FT ECO:0000269|PubMed:32194979"
FT BINDING 218
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00763,
FT ECO:0000269|PubMed:32194979"
FT BINDING 231
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00763,
FT ECO:0000269|PubMed:32194979"
FT BINDING 233
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00763,
FT ECO:0000269|PubMed:32194979"
FT BINDING 271
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:32194979"
FT DISULFID 16..20
FT /evidence="ECO:0000269|PubMed:32194979"
FT MUTAGEN 16
FT /note="C->A: 6-fold decrease in DNA binding and 2-fold
FT decrease in cleavage activities; when associated with A-
FT 20."
FT /evidence="ECO:0000269|PubMed:32194979"
FT MUTAGEN 20
FT /note="C->A: 6-fold decrease in DNA binding and 2-fold
FT decrease in cleavage activities; when associated with A-
FT 16."
FT /evidence="ECO:0000269|PubMed:32194979"
FT STRAND 1..5
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 8..11
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 20..34
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 41..44
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 49..52
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 58..71
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 74..78
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 91..107
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 111..115
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 121..129
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 138..142
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 147..150
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 156..169
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 173..179
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 180..185
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 193..204
FT /evidence="ECO:0007829|PDB:6KI3"
FT TURN 205..209
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 212..214
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 215..218
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 221..224
FT /evidence="ECO:0007829|PDB:6KI3"
FT TURN 236..238
FT /evidence="ECO:0007829|PDB:6KHY"
FT TURN 240..242
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 243..245
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 246..248
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 249..251
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 253..264
FT /evidence="ECO:0007829|PDB:6KI3"
FT STRAND 267..270
FT /evidence="ECO:0007829|PDB:6KI3"
FT HELIX 277..295
FT /evidence="ECO:0007829|PDB:6KI3"
SQ SEQUENCE 296 AA; 33482 MW; 13BF4E258EC5A641 CRC64;
MFGAFVSHRL WSDSGCTTTC ITNSIANYVA FGEQIGFPFK SAQVFIAGPR KAVINIQEDD
KVELLKMIVK HNLWVVAHGT YLDVPWSRRS AFVTHFIQQE LLICKEVGIK GLVLHLGAVE
PELIVEGLKK IKPVEGVVIY LETPHNKHHT YKYSTMEQIK ELFLRIRNTR LKQIGLCIDT
AHIWSSGVNI SSYNDAGQWL RSLENIHSVI PPSHIMFHLN DAATECGSGI DRHASLFEGM
IWKSYSHKIK QSGLYCFVEY ITRHQCPAIL ERNLGSSMQL QTALTAEFTT LKSLLK
