POLX_BACSU
ID POLX_BACSU Reviewed; 570 AA.
AC P94544; Q795X4;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1997, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=DNA polymerase/3'-5' exonuclease PolX;
DE Includes:
DE RecName: Full=DNA polymerase type-X;
DE EC=2.7.7.7;
DE Includes:
DE RecName: Full=3'-5' exodeoxyribonuclease;
DE Short=3'-5' exonuclease;
DE EC=3.1.11.1;
GN Name=polX; Synonyms=yshC; OrderedLocusNames=BSU28590;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=8969504; DOI=10.1099/13500872-142-11-3067;
RA Wipat A., Carter N., Brignell C.S., Guy J.B., Piper K., Sanders J.,
RA Emmerson P.T., Harwood C.R.;
RT "The dnaB-pheA (256 degrees-240 degrees) region of the Bacillus subtilis
RT chromosome containing genes responsible for stress responses, the
RT utilization of plant cell walls and primary metabolism.";
RL Microbiology 142:3067-3078(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP FUNCTION, DNA POLYMERASE ACTIVITY, COFACTOR, SUBUNIT, ACTIVITY REGULATION,
RP AND MUTAGENESIS OF 193-ASP--ASP-195.
RX PubMed=18938175; DOI=10.1016/j.jmb.2008.09.081;
RA Banos B., Lazaro J.M., Villar L., Salas M., de Vega M.;
RT "Characterization of a Bacillus subtilis 64-kDa DNA polymerase X
RT potentially involved in DNA repair.";
RL J. Mol. Biol. 384:1019-1028(2008).
RN [4]
RP FUNCTION, EXONUCLEASE ACTIVITY, COFACTOR, DOMAIN, AND MUTAGENESIS OF
RP 339-HIS--HIS-341.
RX PubMed=18776221; DOI=10.1093/nar/gkn526;
RA Banos B., Lazaro J.M., Villar L., Salas M., de Vega M.;
RT "Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease
RT activity residing in the PHP domain of a family X DNA polymerase.";
RL Nucleic Acids Res. 36:5736-5749(2008).
CC -!- FUNCTION: Strictly DNA-template-directed DNA polymerase, preferentially
CC acting on DNA structures containing gaps from one to a few nucleotides
CC and bearing a phosphate group at the 5' end of the downstream DNA. The
CC fact that PolX is able to conduct filling of a single-nucleotide gap,
CC allowing further sealing of the resulting nick by a DNA ligase, points
CC to a putative role in base excision repair (BER) during the B.subtilis
CC life cycle. Moreover, also possesses a 3'-5' exonuclease activity able
CC to edit unpaired 3'-termini in a gapped DNA substrate and likely
CC involved in resecting unannealed 3'-termini during DNA repair. The same
CC PolX molecule could perform the subsequent gap-filling step. Does not
CC display 5'-deoxyribose 5'-phosphate (dRP) lyase activity, as predicted
CC by the lack of the lysine and tyrosine residues responsible for the dRP
CC lyase activity in some other PolX members.
CC {ECO:0000269|PubMed:18776221, ECO:0000269|PubMed:18938175}.
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 -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC nucleoside 5'-phosphates.; EC=3.1.11.1;
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000305};
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000305};
CC Note=Probably binds 2 divalent metal cations per N-terminal polymerase
CC domain. Mn(2+) is more effective than Mg(2+) for DNA polymerase
CC activity. {ECO:0000305};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000305};
CC Note=Probably binds 3 Mn(2+) ions per C-terminal exonuclease domain.
CC Mg(2+) cannot replace Mn(2+) for 3'-5' exonuclease activity.
CC {ECO:0000305};
CC -!- ACTIVITY REGULATION: The polymerization activity is inhibited in the
CC presence of 2'-3'-dideoxynucleoside 5'-triphosphate (ddNTP).
CC {ECO:0000269|PubMed:18938175}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:18938175}.
CC -!- DOMAIN: The 3'-5' exonuclease activity resides in the C-terminal PHP
CC domain. {ECO:0000269|PubMed:18776221}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the DNA polymerase
CC type-X family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the PHP family.
CC {ECO:0000305}.
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DR EMBL; Z75208; CAA99568.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB14819.1; -; Genomic_DNA.
DR PIR; C69985; C69985.
DR RefSeq; NP_390737.1; NC_000964.3.
DR RefSeq; WP_003229538.1; NZ_JNCM01000036.1.
DR AlphaFoldDB; P94544; -.
DR SMR; P94544; -.
DR STRING; 224308.BSU28590; -.
DR PaxDb; P94544; -.
DR PRIDE; P94544; -.
DR DNASU; 937426; -.
DR EnsemblBacteria; CAB14819; CAB14819; BSU_28590.
DR GeneID; 937426; -.
DR KEGG; bsu:BSU28590; -.
DR PATRIC; fig|224308.179.peg.3106; -.
DR eggNOG; COG1387; Bacteria.
DR eggNOG; COG1796; Bacteria.
DR InParanoid; P94544; -.
DR OMA; HNVRMRQ; -.
DR PhylomeDB; P94544; -.
DR BioCyc; BSUB:BSU28590-MON; -.
DR BRENDA; 2.7.7.7; 658.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IBA:GO_Central.
DR GO; GO:0008852; F:exodeoxyribonuclease I activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR CDD; cd00141; NT_POLXc; 1.
DR Gene3D; 1.10.150.110; -; 1.
DR Gene3D; 3.30.210.10; -; 1.
DR Gene3D; 3.30.460.10; -; 1.
DR InterPro; IPR002054; DNA-dir_DNA_pol_X.
DR InterPro; IPR010996; DNA_pol_b-like_N.
DR InterPro; IPR027421; DNA_pol_lamdba_lyase_dom_sf.
DR InterPro; IPR037160; DNA_Pol_thumb_sf.
DR InterPro; IPR003583; Hlx-hairpin-Hlx_DNA-bd_motif.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR004013; PHP_dom.
DR InterPro; IPR003141; Pol/His_phosphatase_N.
DR InterPro; IPR016195; Pol/histidinol_Pase-like.
DR InterPro; IPR029398; PolB_thumb.
DR InterPro; IPR022311; UCP005047_YshC.
DR Pfam; PF14791; DNA_pol_B_thumb; 1.
DR Pfam; PF14716; HHH_8; 1.
DR Pfam; PF02811; PHP; 1.
DR PIRSF; PIRSF005047; UCP005047_YshC; 1.
DR SMART; SM00278; HhH1; 3.
DR SMART; SM00481; POLIIIAc; 1.
DR SMART; SM00483; POLXc; 1.
DR SUPFAM; SSF47802; SSF47802; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
DR SUPFAM; SSF89550; SSF89550; 1.
PE 1: Evidence at protein level;
KW DNA damage; DNA repair; DNA replication; DNA synthesis; DNA-binding;
KW DNA-directed DNA polymerase; Hydrolase; Magnesium; Manganese;
KW Metal-binding; Multifunctional enzyme; Nucleotidyltransferase;
KW Reference proteome; Transferase.
FT CHAIN 1..570
FT /note="DNA polymerase/3'-5' exonuclease PolX"
FT /id="PRO_0000360771"
FT REGION 1..315
FT /note="DNA polymerase type-X"
FT REGION 333..570
FT /note="3'-5' exonuclease"
FT BINDING 193
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 193
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000305"
FT BINDING 195
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 195
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000305"
FT BINDING 240
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 339
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 341
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000305"
FT BINDING 371
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 410
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 410
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 437
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 465
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000250"
FT BINDING 526
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 528
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT MUTAGEN 193..195
FT /note="DLD->ALA: Abolishes DNA polymerase activity."
FT /evidence="ECO:0000269|PubMed:18938175"
FT MUTAGEN 339..341
FT /note="HMH->AMA: Abolishes 3'-5' exonuclease activity.
FT Still possesses DNA polymerase activity."
FT /evidence="ECO:0000269|PubMed:18776221"
SQ SEQUENCE 570 AA; 64120 MW; 06AEA028BFA3D3F5 CRC64;
MHKKDIIRLL ETIAVYMELK GDNPFKVSAF RKAAAALEQD DRSLSEMDDM MSLSGIGKGT
YSVIKEYIDE GKSSTLESLQ KEVPEGLVPL LKLPGLGGKK IAKLYKELGV HDAESLKEAC
EQQKVQGLAG FGKKSEEKIL QALGEAGKQP ERFPIGYALR IAREIEEHLS QFTHIIKFSR
AGSLRRARET VKDLDYIIAT DHPAEVREQL LELPNIKSVI ASGDTKVSVI LSFEYETSVD
FRLVTEEQFP TTLHHFTGSK DHNIKMRQIA KERGERISEY GVETVETGEI KTFPSEREFY
AHFGLPLIPP EIRESGQEVE TYSDSIELIE LGQIKGDLHM HSTWSDGAFS IREMAEACIK
KGYQYMAITD HSQYLKVANG LTAERLKQQA KEIDALNAEF ENFRILKGVE MDILPDGTLD
YDDDVLAEMD IVIASIHSSF NQPEHVIMKR LETALTNKHV DIIAHPTGRL IGRRAGYEID
IDQLIELARK TNTALELNAN PARLDLRTEH LMKANEQGVT LVINTDAHNI EMLDDMKTGV
TAARKGWTET KNVLNARSLK DVEAFLKRND
