DPOLX_ASFB7
ID DPOLX_ASFB7 Reviewed; 174 AA.
AC P42494;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=Repair DNA polymerase X;
DE Short=Pol X;
DE EC=2.7.7.7 {ECO:0000269|PubMed:17144676, ECO:0000269|PubMed:24617852};
DE AltName: Full=AsfvPolX;
GN OrderedLocusNames=Ba71V-97; ORFNames=O174L;
OS African swine fever virus (strain Badajoz 1971 Vero-adapted) (Ba71V)
OS (ASFV).
OC Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota; Pokkesviricetes;
OC Asfuvirales; Asfarviridae; Asfivirus.
OX NCBI_TaxID=10498;
OH NCBI_TaxID=6937; Ornithodoros (relapsing fever ticks).
OH NCBI_TaxID=9823; Sus scrofa (Pig).
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=11831707; DOI=10.1006/viro.1995.1149;
RA Yanez R.J., Rodriguez J.M., Nogal M.L., Yuste L., Enriquez C.,
RA Rodriguez J.F., Vinuela E.;
RT "Analysis of the complete nucleotide sequence of African swine fever
RT virus.";
RL Virology 208:249-278(1995).
RN [2]
RP FUNCTION.
RX PubMed=12595253; DOI=10.1016/s0022-2836(03)00019-6;
RA Garcia-Escudero R., Garcia-Diaz M., Salas M.L., Blanco L., Salas J.;
RT "DNA polymerase X of African swine fever virus: insertion fidelity on
RT gapped DNA substrates and AP lyase activity support a role in base excision
RT repair of viral DNA.";
RL J. Mol. Biol. 326:1403-1412(2003).
RN [3]
RP CATALYTIC ACTIVITY.
RX PubMed=17144676; DOI=10.1021/bi0613325;
RA Lamarche B.J., Kumar S., Tsai M.-D.;
RT "ASFV DNA polymerase X is extremely error-prone under diverse assay
RT conditions and within multiple DNA sequence contexts.";
RL Biochemistry 45:14826-14833(2006).
RN [4]
RP CHARACTERIZATION.
RX PubMed=17941646; DOI=10.1021/bi700677j;
RA Jezewska M.J., Bujalowski P.J., Bujalowski W.;
RT "Interactions of the DNA polymerase X from African swine fever virus with
RT gapped DNA substrates. Quantitative analysis of functional structures of
RT the formed complexes.";
RL Biochemistry 46:12909-12924(2007).
RN [5]
RP CHARACTERIZATION, AND DNA-BINDING.
RX PubMed=17765921; DOI=10.1016/j.jmb.2007.06.054;
RA Jezewska M.J., Bujalowski P.J., Bujalowski W.;
RT "Interactions of the DNA polymerase X of African swine fever virus with
RT double-stranded DNA. Functional structure of the complex.";
RL J. Mol. Biol. 373:75-95(2007).
RN [6]
RP SUBCELLULAR LOCATION.
RX PubMed=30185597; DOI=10.1128/jvi.01293-18;
RA Alejo A., Matamoros T., Guerra M., Andres G.;
RT "A Proteomic Atlas of the African Swine Fever Virus Particle.";
RL J. Virol. 92:0-0(2018).
RN [7]
RP STRUCTURE BY NMR.
RX PubMed=11685238; DOI=10.1038/nsb1101-936;
RA Maciejewski M.W., Shin R., Pan B., Marintchev A., Denninger A.,
RA Mullen M.A., Chen K., Gryk M.R., Mullen G.P.;
RT "Solution structure of a viral DNA repair polymerase.";
RL Nat. Struct. Biol. 8:936-941(2001).
RN [8]
RP STRUCTURE BY NMR, FUNCTION, DOMAIN, DISULFIDE BOND, AND COFACTOR.
RX PubMed=11685239; DOI=10.1038/nsb1101-942;
RA Showalter A.K., Byeon I.-J., Su M.-I., Tsai M.-D.;
RT "Solution structure of a viral DNA polymerase X and evidence for a
RT mutagenic function.";
RL Nat. Struct. Biol. 8:942-946(2001).
RN [9] {ECO:0007744|PDB:2M2T, ECO:0007744|PDB:2M2U, ECO:0007744|PDB:2M2V, ECO:0007744|PDB:2M2W}
RP STRUCTURE BY NMR, MUTAGENESIS OF HIS-115, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, FUNCTION, AND DOMAIN.
RX PubMed=24617852; DOI=10.1021/ja4102375;
RA Wu W.J., Su M.I., Wu J.L., Kumar S., Lim L.H., Wang C.W., Nelissen F.H.,
RA Chen M.C., Doreleijers J.F., Wijmenga S.S., Tsai M.D.;
RT "How a low-fidelity DNA polymerase chooses non-Watson-Crick from Watson-
RT Crick incorporation.";
RL J. Am. Chem. Soc. 136:4927-4937(2014).
RN [10] {ECO:0007744|PDB:5HR9, ECO:0007744|PDB:5HRB, ECO:0007744|PDB:5HRD, ECO:0007744|PDB:5HRE, ECO:0007744|PDB:5HRF, ECO:0007744|PDB:5HRG, ECO:0007744|PDB:5HRH, ECO:0007744|PDB:5HRI, ECO:0007744|PDB:5HRK, ECO:0007744|PDB:5HRL}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH MANGANESE,
RP MUTAGENESIS OF HIS-115; ARG-125; ARG-127 AND ARG-168, COFACTOR, AND
RP FUNCTION.
RX PubMed=28245220; DOI=10.1371/journal.pbio.1002599;
RA Chen Y., Zhang J., Liu H., Gao Y., Li X., Zheng L., Cui R., Yao Q.,
RA Rong L., Li J., Huang Z., Ma J., Gan J.;
RT "Unique 5'-P recognition and basis for dG:dGTP misincorporation of ASFV DNA
RT polymerase X.";
RL PLoS Biol. 15:e1002599-e1002599(2017).
RN [11] {ECO:0007744|PDB:5XM8, ECO:0007744|PDB:5XM9, ECO:0007744|PDB:5XMA}
RP X-RAY CRYSTALLOGRAPHY (2.55 ANGSTROMS).
RX PubMed=29222499; DOI=10.1038/s41467-017-02203-x;
RA Liu H., Yu X., Chen Y., Zhang J., Wu B., Zheng L., Haruehanroengra P.,
RA Wang R., Li S., Lin J., Li J., Sheng J., Huang Z., Ma J., Gan J.;
RT "Crystal structure of an RNA-cleaving DNAzyme.";
RL Nat. Commun. 8:2006-2006(2017).
CC -!- FUNCTION: Error-prone polymerase lacking a proofreading 3'-5'
CC exonuclease which catalyzes the gap-filling reaction during the DNA
CC repair process (PubMed:11685239, PubMed:28245220). Specifically binds
CC intermediates in the single-nucleotide base-excision repair process
CC (PubMed:12595253). Also catalyzes DNA polymerization with low
CC nucleotide-insertion fidelity (PubMed:24617852). Probably acts as a
CC strategic DNA mutase, which gives rise to a rapid emergence of variants
CC (PubMed:11685239). Generates mismatched G-G pairs, in that case, the
CC polymerase first binds the deoxynucleotide followed by mismatch
CC formation (PubMed:24617852). Together with the viral DNA ligase, fills
CC the single nucleotide gaps generated by the AP endonuclease (Probable).
CC Binds DNA with high affinity via the helix alphaE (PubMed:24617852).
CC {ECO:0000269|PubMed:11685239, ECO:0000269|PubMed:12595253,
CC ECO:0000269|PubMed:24617852, ECO:0000269|PubMed:28245220, ECO:0000305}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) =
CC diphosphate + DNA(n+1); Xref=Rhea:RHEA:22508, Rhea:RHEA-COMP:17339,
CC Rhea:RHEA-COMP:17340, ChEBI:CHEBI:33019, ChEBI:CHEBI:61560,
CC ChEBI:CHEBI:173112; EC=2.7.7.7;
CC Evidence={ECO:0000269|PubMed:24617852};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11685239, ECO:0000269|PubMed:28245220};
CC Note=In the presence of magnesium, pol X shows a strong preference for
CC the ssDNA gaps having one and two nucleotides.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.26 uM for dGTP {ECO:0000269|PubMed:24617852};
CC KM=0.46 uM for dATP {ECO:0000269|PubMed:24617852};
CC KM=9.4 uM for dCTP {ECO:0000269|PubMed:24617852};
CC KM=8.6 uM for dTTP {ECO:0000269|PubMed:24617852};
CC -!- SUBCELLULAR LOCATION: Virion {ECO:0000269|PubMed:30185597}. Note=Found
CC in association with viral nucleoid. {ECO:0000269|PubMed:30185597}.
CC -!- DOMAIN: Small DNA polymerase formed from only a palm and a C-terminal
CC subdomain (PubMed:11685239). Unlike other polymerases, binds DNA via
CC the helix alphaE (PubMed:24617852). The total DNA-binding site of pol X
CC is composed of two DNA-binding subsites. {ECO:0000269|PubMed:11685239,
CC ECO:0000269|PubMed:24617852}.
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:0000305}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-X family. {ECO:0000305}.
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DR EMBL; U18466; AAA65326.1; -; Genomic_DNA.
DR RefSeq; NP_042790.1; NC_001659.2.
DR PDB; 1JAJ; NMR; -; A=1-174.
DR PDB; 1JQR; NMR; -; A=1-174.
DR PDB; 2M2T; NMR; -; A=1-174.
DR PDB; 2M2U; NMR; -; A=1-174.
DR PDB; 2M2V; NMR; -; A=1-174.
DR PDB; 2M2W; NMR; -; A=1-174.
DR PDB; 5HR9; X-ray; 2.20 A; A/B=1-174.
DR PDB; 5HRB; X-ray; 1.70 A; A=1-174.
DR PDB; 5HRD; X-ray; 1.80 A; A/B/C/D=1-174.
DR PDB; 5HRE; X-ray; 1.75 A; A=1-174.
DR PDB; 5HRF; X-ray; 2.25 A; A/B=1-174.
DR PDB; 5HRG; X-ray; 2.00 A; A/B=1-174.
DR PDB; 5HRH; X-ray; 3.00 A; A/B=1-174.
DR PDB; 5HRI; X-ray; 2.20 A; A/B=1-174.
DR PDB; 5HRK; X-ray; 2.90 A; A/B=1-174.
DR PDB; 5HRL; X-ray; 2.40 A; A/B=1-174.
DR PDB; 5XM8; X-ray; 2.55 A; A/B/C/D=1-174.
DR PDB; 5XM9; X-ray; 3.05 A; A/B/C/D=1-174.
DR PDB; 5XMA; X-ray; 3.80 A; A/B=1-174.
DR PDB; 7CPW; X-ray; 2.85 A; A/B=1-174.
DR PDBsum; 1JAJ; -.
DR PDBsum; 1JQR; -.
DR PDBsum; 2M2T; -.
DR PDBsum; 2M2U; -.
DR PDBsum; 2M2V; -.
DR PDBsum; 2M2W; -.
DR PDBsum; 5HR9; -.
DR PDBsum; 5HRB; -.
DR PDBsum; 5HRD; -.
DR PDBsum; 5HRE; -.
DR PDBsum; 5HRF; -.
DR PDBsum; 5HRG; -.
DR PDBsum; 5HRH; -.
DR PDBsum; 5HRI; -.
DR PDBsum; 5HRK; -.
DR PDBsum; 5HRL; -.
DR PDBsum; 5XM8; -.
DR PDBsum; 5XM9; -.
DR PDBsum; 5XMA; -.
DR PDBsum; 7CPW; -.
DR BMRB; P42494; -.
DR SMR; P42494; -.
DR GeneID; 22220326; -.
DR KEGG; vg:22220326; -.
DR BRENDA; 2.7.7.7; 176.
DR EvolutionaryTrace; P42494; -.
DR Proteomes; UP000000624; Genome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:CACAO.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR Gene3D; 3.30.210.10; -; 1.
DR Gene3D; 3.30.460.10; -; 1.
DR InterPro; IPR019843; DNA_pol-X_BS.
DR InterPro; IPR037160; DNA_Pol_thumb_sf.
DR InterPro; IPR022312; DNA_pol_X.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR029398; PolB_thumb.
DR PANTHER; PTHR11276; PTHR11276; 1.
DR Pfam; PF14791; DNA_pol_B_thumb; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
DR PROSITE; PS00522; DNA_POLYMERASE_X; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Disulfide bond; DNA damage; DNA repair; DNA-binding;
KW DNA-directed DNA polymerase; Magnesium; Metal-binding;
KW Nucleotidyltransferase; Reference proteome; Transferase; Virion.
FT CHAIN 1..174
FT /note="Repair DNA polymerase X"
FT /id="PRO_0000218798"
FT REGION 42..51
FT /note="Involved in ssDNA binding"
FT /evidence="ECO:0000250"
FT BINDING 49
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:11685239,
FT ECO:0000305|PubMed:28245220"
FT BINDING 51
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:11685239,
FT ECO:0000305|PubMed:28245220"
FT BINDING 100
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:11685239,
FT ECO:0000305|PubMed:28245220"
FT SITE 115
FT /note="Stabilizes dGTP in a syn confromation to overcome
FT the Watson-Crick base pairing constraint"
FT /evidence="ECO:0000269|PubMed:24617852"
FT DISULFID 81..86
FT /evidence="ECO:0000269|PubMed:11685239"
FT MUTAGEN 115
FT /note="H->A: Complete loss of MgdGTP binding and dG:dGTP
FT ternary complex formation but not dG:dCTP ternary complex
FT formation."
FT /evidence="ECO:0000269|PubMed:24617852"
FT MUTAGEN 115
FT /note="H->D: 18x decreased dG:dGTP misincorporation."
FT /evidence="ECO:0000269|PubMed:24617852"
FT MUTAGEN 115
FT /note="H->E: 36x decreased dG:dGTP misincorporation."
FT /evidence="ECO:0000269|PubMed:24617852"
FT MUTAGEN 115
FT /note="H->F: Slower dG:dGTP misincorporation."
FT /evidence="ECO:0000269|PubMed:24617852"
FT MUTAGEN 125
FT /note="R->A: Loss of DNA binding affinity. Decreased
FT dG:dGTP misincorporation."
FT /evidence="ECO:0000269|PubMed:28245220"
FT MUTAGEN 127
FT /note="R->A: Slower dG:dGTP misincorporation."
FT /evidence="ECO:0000269|PubMed:28245220"
FT MUTAGEN 168
FT /note="R->A: Loss of DNA binding affinity. Decreased dGTP
FT misincorporation."
FT /evidence="ECO:0000269|PubMed:28245220"
FT HELIX 4..14
FT /evidence="ECO:0007829|PDB:5HRB"
FT TURN 15..17
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 18..22
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 25..28
FT /evidence="ECO:0007829|PDB:5HRB"
FT HELIX 31..33
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:5HRB"
FT HELIX 38..41
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 45..57
FT /evidence="ECO:0007829|PDB:5HRB"
FT HELIX 59..64
FT /evidence="ECO:0007829|PDB:5HRB"
FT HELIX 66..68
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 69..71
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 76..81
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 83..92
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 95..105
FT /evidence="ECO:0007829|PDB:5HRB"
FT HELIX 106..108
FT /evidence="ECO:0007829|PDB:5HRB"
FT HELIX 109..117
FT /evidence="ECO:0007829|PDB:5HRB"
FT HELIX 120..132
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 135..138
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 141..144
FT /evidence="ECO:0007829|PDB:5HRB"
FT STRAND 147..149
FT /evidence="ECO:0007829|PDB:1JAJ"
FT HELIX 156..162
FT /evidence="ECO:0007829|PDB:5HRB"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:5HRB"
SQ SEQUENCE 174 AA; 20314 MW; 48E24A0ACDC0F9C7 CRC64;
MLTLIQGKKI VNHLRSRLAF EYNGQLIKIL SKNIVAVGSL RREEKMLNDV DLLIIVPEKK
LLKHVLPNIR IKGLSFSVKV CGERKCVLFI EWEKKTYQLD LFTALAEEKP YAIFHFTGPV
SYLIRIRAAL KKKNYKLNQY GLFKNQTLVP LKITTEKELI KELGFTYRIP KKRL
