ID D9N168_GEOSE Unreviewed; 579 AA. AC D9N168; DT 05-OCT-2010, integrated into UniProtKB/TrEMBL. DT 05-OCT-2010, sequence version 1. DT 27-MAR-2024, entry version 58. DE RecName: Full=DNA polymerase I {ECO:0000256|ARBA:ARBA00020311, ECO:0000256|RuleBase:RU004460}; DE EC=2.7.7.7 {ECO:0000256|RuleBase:RU004460}; GN Name=DPO1 {ECO:0000313|PDB:3HT3}; GN Synonyms=polA {ECO:0000256|RuleBase:RU004460}; OS Geobacillus stearothermophilus (Bacillus stearothermophilus). OC Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Geobacillus. OX NCBI_TaxID=1422 {ECO:0000313|PDB:3HT3}; RN [1] {ECO:0007829|PDB:3HPO, ECO:0007829|PDB:3HT3} RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH TTP. RX PubMed=21454515; DOI=10.1074/jbc.M110.191130; RA Wu E.Y., Beese L.S.; RT "The structure of a high fidelity DNA polymerase bound to a mismatched RT nucleotide reveals an "ajar" intermediate conformation in the nucleotide RT selection mechanism."; RL J. Biol. Chem. 286:19758-19767(2011). RN [2] {ECO:0007829|PDB:4O0I} RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS). RA Jiang S., Gan J., Sun H., Huang Z.; RT "Crystal structure of fragment DNA polymerase I from Bacillus RT stearothermophilus with 2'-MeSe-arabino-guanosine derivatized DNA."; RL Submitted (DEC-2013) to the PDB data bank. RN [3] {ECO:0007829|PDB:6UEU} RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH DATP. RA Walsh A.R., Beese L.S., Wu E.Y.; RT "Structural basis for blockage of DNA synthesis by a thymine dimer lesion RT in a high-fidelity DNA polymerase."; RL Submitted (SEP-2019) to the PDB data bank. RN [4] {ECO:0007829|PDB:6P5C} RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS). RX PubMed=32113909; DOI=10.1016/j.dnarep.2020.102826; RA Hamm M.L., Garcia A.A., Gilbert R., Johri M., Ricart M., Sholes S.L., RA Murray-Nerger L.A., Wu E.Y.; RT "The importance of Ile716 toward the mutagenicity of 8-Oxo-2'- RT deoxyguanosine with Bacillus fragment DNA polymerase."; RL DNA Repair 89:102826-102826(2020). RN [5] {ECO:0007829|PDB:6UR2, ECO:0007829|PDB:6UR4} RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH CA(2+) AND MN(2+). RX PubMed=32188786; DOI=10.1073/pnas.1922400117; RA Lelyveld V.S., Zhang W., Szostak J.W.; RT "Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase."; RL Proc. Natl. Acad. Sci. U.S.A. 117:7276-7283(2020). RN [6] {ECO:0007829|PDB:8SCG, ECO:0007829|PDB:8SCI} RP X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) IN COMPLEX WITH CA(2+) AND DGTP. RX PubMed=37883544; DOI=10.1126/science.adh5339; RA Lelyveld V.S., Fang Z., Szostak J.W.; RT "Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase RT activity."; RL Science 382:423-429(2023). CC -!- FUNCTION: In addition to polymerase activity, this DNA polymerase CC exhibits 5'-3' exonuclease activity. {ECO:0000256|RuleBase:RU004460}. 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:0000256|ARBA:ARBA00024632, CC ECO:0000256|RuleBase:RU004460}; CC -!- SUBUNIT: Single-chain monomer with multiple functions. CC {ECO:0000256|RuleBase:RU004460}. CC -!- SIMILARITY: Belongs to the DNA polymerase type-A family. CC {ECO:0000256|ARBA:ARBA00007705, ECO:0000256|RuleBase:RU004460}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR PDB; 3HPO; X-ray; 1.75 A; A=1-579. DR PDB; 3HT3; X-ray; 1.70 A; A/D=1-579. DR PDB; 4O0I; X-ray; 2.20 A; A=1-579. DR PDB; 6P5C; X-ray; 2.20 A; A=1-579. DR PDB; 6UEU; X-ray; 1.80 A; A/D=1-579. DR PDB; 6UR2; X-ray; 2.27 A; A=1-579. DR PDB; 6UR4; X-ray; 2.25 A; A=1-579. DR PDB; 6UR9; X-ray; 2.10 A; A/D=1-579. DR PDB; 6US5; X-ray; 2.25 A; A/D=1-579. DR PDB; 8SCG; X-ray; 2.00 A; A/D=1-579. DR PDB; 8SCI; X-ray; 2.67 A; A/D=1-579. DR PDB; 8SCJ; X-ray; 2.68 A; A/D=1-579. DR PDB; 8SCK; X-ray; 2.30 A; A/D=1-579. DR PDB; 8SCL; X-ray; 2.44 A; A/D=1-579. DR PDB; 8SCM; X-ray; 2.30 A; A/D=1-579. DR PDB; 8SCN; X-ray; 2.30 A; A/D=1-579. DR PDB; 8SCO; X-ray; 1.92 A; A/D=1-579. DR PDB; 8SCP; X-ray; 2.08 A; A/D=1-579. DR PDB; 8SCQ; X-ray; 2.18 A; A/D=1-579. DR PDB; 8SCR; X-ray; 2.00 A; A/D=1-579. DR PDB; 8SCS; X-ray; 2.10 A; A/D=1-579. DR PDB; 8SCT; X-ray; 2.34 A; A/D=1-579. DR PDB; 8SCU; X-ray; 2.38 A; A/D=1-579. DR PDBsum; 3HT3; -. DR PDBsum; 4O0I; -. DR PDBsum; 6P5C; -. DR PDBsum; 6UR2; -. DR PDBsum; 6UR4; -. DR PDBsum; 6UR9; -. DR PDBsum; 6US5; -. DR AlphaFoldDB; D9N168; -. DR SMR; D9N168; -. DR EvolutionaryTrace; D9N168; -. DR GO; GO:0008408; F:3'-5' exonuclease activity; IEA:InterPro. DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule. DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-UniRule. DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW. DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-UniRule. DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule. DR CDD; cd08637; DNA_pol_A_pol_I_C; 1. DR CDD; cd06128; DNA_polA_exo; 1. DR Gene3D; 3.30.70.370; -; 1. DR Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 1. DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 1. DR InterPro; IPR002562; 3'-5'_exonuclease_dom. DR InterPro; IPR019760; DNA-dir_DNA_pol_A_CS. DR InterPro; IPR001098; DNA-dir_DNA_pol_A_palm_dom. DR InterPro; IPR043502; DNA/RNA_pol_sf. DR InterPro; IPR018320; DNA_polymerase_1. DR InterPro; IPR002298; DNA_polymerase_A. DR InterPro; IPR012337; RNaseH-like_sf. DR InterPro; IPR036397; RNaseH_sf. DR NCBIfam; TIGR00593; pola; 1. DR PANTHER; PTHR10133; DNA POLYMERASE I; 1. DR PANTHER; PTHR10133:SF62; DNA POLYMERASE THETA; 1. DR Pfam; PF00476; DNA_pol_A; 1. DR PRINTS; PR00868; DNAPOLI. DR SMART; SM00474; 35EXOc; 1. DR SMART; SM00482; POLAc; 1. DR SUPFAM; SSF56672; DNA/RNA polymerases; 1. DR SUPFAM; SSF53098; Ribonuclease H-like; 1. DR PROSITE; PS00447; DNA_POLYMERASE_A; 1. PE 1: Evidence at protein level; KW 3D-structure {ECO:0007829|PDB:3HPO, ECO:0007829|PDB:3HT3}; KW Calcium {ECO:0007829|PDB:6UR9, ECO:0007829|PDB:8SCG}; KW DNA damage {ECO:0000256|RuleBase:RU004460}; KW DNA repair {ECO:0000256|RuleBase:RU004460}; KW DNA replication {ECO:0000256|RuleBase:RU004460}; KW DNA-binding {ECO:0000256|RuleBase:RU004460}; KW DNA-directed DNA polymerase {ECO:0000256|RuleBase:RU004460}; KW Hydrolase {ECO:0000256|ARBA:ARBA00022801}; KW Metal-binding {ECO:0007829|PDB:6UR9, ECO:0007829|PDB:6US5}; KW Nucleotide-binding {ECO:0007829|PDB:3HPO}; KW Nucleotidyltransferase {ECO:0000256|RuleBase:RU004460}; KW Transferase {ECO:0000256|RuleBase:RU004460}. FT DOMAIN 3..169 FT /note="3'-5' exonuclease" FT /evidence="ECO:0000259|SMART:SM00474" FT DOMAIN 336..543 FT /note="DNA-directed DNA polymerase family A palm" FT /evidence="ECO:0000259|SMART:SM00482" FT BINDING 318 FT /ligand="dATP" FT /ligand_id="ChEBI:CHEBI:61404" FT /evidence="ECO:0007829|PDB:6UEU" FT BINDING 318 FT /ligand="dGTP" FT /ligand_id="ChEBI:CHEBI:61429" FT /evidence="ECO:0007829|PDB:8SCG, ECO:0007829|PDB:8SCI" FT BINDING 356 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="1" FT /evidence="ECO:0007829|PDB:6UR9, ECO:0007829|PDB:8SCG" FT BINDING 356 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="2" FT /evidence="ECO:0007829|PDB:8SCI" FT BINDING 356 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /evidence="ECO:0007829|PDB:6US5" FT BINDING 357 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="1" FT /evidence="ECO:0007829|PDB:6UR9, ECO:0007829|PDB:8SCG" FT BINDING 357 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /evidence="ECO:0007829|PDB:6US5" FT BINDING 358 FT /ligand="dGTP" FT /ligand_id="ChEBI:CHEBI:61429" FT /evidence="ECO:0007829|PDB:8SCL, ECO:0007829|PDB:8SCM" FT BINDING 359 FT /ligand="dATP" FT /ligand_id="ChEBI:CHEBI:61404" FT /evidence="ECO:0007829|PDB:6UEU" FT BINDING 359 FT /ligand="dCTP" FT /ligand_id="ChEBI:CHEBI:61481" FT /evidence="ECO:0007829|PDB:3HT3" FT BINDING 359 FT /ligand="dGTP" FT /ligand_id="ChEBI:CHEBI:61429" FT /evidence="ECO:0007829|PDB:8SCG, ECO:0007829|PDB:8SCI" FT BINDING 359 FT /ligand="dTTP" FT /ligand_id="ChEBI:CHEBI:37568" FT /evidence="ECO:0007829|PDB:3HPO" FT BINDING 360 FT /ligand="dGTP" FT /ligand_id="ChEBI:CHEBI:61429" FT /evidence="ECO:0007829|PDB:8SCO, ECO:0007829|PDB:8SCP" FT BINDING 361 FT /ligand="dATP" FT /ligand_id="ChEBI:CHEBI:61404" FT /evidence="ECO:0007829|PDB:6UEU" FT BINDING 361 FT /ligand="dGTP" FT /ligand_id="ChEBI:CHEBI:61429" FT /evidence="ECO:0007829|PDB:8SCG, ECO:0007829|PDB:8SCJ" FT BINDING 385 FT /ligand="dATP" FT /ligand_id="ChEBI:CHEBI:61404" FT /evidence="ECO:0007829|PDB:6UEU" FT BINDING 385 FT /ligand="dCTP" FT /ligand_id="ChEBI:CHEBI:61481" FT /evidence="ECO:0007829|PDB:3HT3" FT BINDING 385 FT /ligand="dGTP" FT /ligand_id="ChEBI:CHEBI:61429" FT /evidence="ECO:0007829|PDB:8SCG, ECO:0007829|PDB:8SCI" FT BINDING 385 FT /ligand="dTTP" FT /ligand_id="ChEBI:CHEBI:37568" FT /evidence="ECO:0007829|PDB:3HPO" FT BINDING 405 FT /ligand="dATP" FT /ligand_id="ChEBI:CHEBI:61404" FT /evidence="ECO:0007829|PDB:6UEU" FT BINDING 405 FT /ligand="dCTP" FT /ligand_id="ChEBI:CHEBI:61481" FT /evidence="ECO:0007829|PDB:3HT3" FT BINDING 405 FT /ligand="dGTP" FT /ligand_id="ChEBI:CHEBI:61429" FT /evidence="ECO:0007829|PDB:8SCG, ECO:0007829|PDB:8SCI" FT BINDING 405 FT /ligand="dTTP" FT /ligand_id="ChEBI:CHEBI:37568" FT /evidence="ECO:0007829|PDB:3HPO" FT BINDING 409 FT /ligand="dATP" FT /ligand_id="ChEBI:CHEBI:61404" FT /evidence="ECO:0007829|PDB:6UEU" FT BINDING 409 FT /ligand="dCTP" FT /ligand_id="ChEBI:CHEBI:61481" FT /evidence="ECO:0007829|PDB:3HT3" FT BINDING 409 FT /ligand="dGTP" FT /ligand_id="ChEBI:CHEBI:61429" FT /evidence="ECO:0007829|PDB:8SCG, ECO:0007829|PDB:8SCI" FT BINDING 409 FT /ligand="dTTP" FT /ligand_id="ChEBI:CHEBI:37568" FT /evidence="ECO:0007829|PDB:3HPO" FT BINDING 413 FT /ligand="dCTP" FT /ligand_id="ChEBI:CHEBI:61481" FT /evidence="ECO:0007829|PDB:3HT3" FT BINDING 413 FT /ligand="dGTP" FT /ligand_id="ChEBI:CHEBI:61429" FT /evidence="ECO:0007829|PDB:8SCO" FT BINDING 413 FT /ligand="dTTP" FT /ligand_id="ChEBI:CHEBI:37568" FT /evidence="ECO:0007829|PDB:3HPO" FT BINDING 533 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="2" FT /evidence="ECO:0007829|PDB:8SCI" FT BINDING 533 FT /ligand="Ca(2+)" FT /ligand_id="ChEBI:CHEBI:29108" FT /ligand_label="1" FT /evidence="ECO:0007829|PDB:6UR9, ECO:0007829|PDB:8SCG" FT BINDING 533 FT /ligand="Mn(2+)" FT /ligand_id="ChEBI:CHEBI:29035" FT /evidence="ECO:0007829|PDB:6US5" SQ SEQUENCE 579 AA; 65967 MW; CDEDB059CBA01889 CRC64; KMAFTLADRV TEEMLADKAA LVVEVVEENY HDAPIVGIAV VNEHGRFFLR PETALADPQF VAWLGDETKK KSMFDSKRAA VALKWKGIEL CGVSFDLLLA AYLLDPAQGV DDVAAAAKMK QYEAVRPDEA VYGKGAKRAV PDEPVLAEHL VRKAAAIWEL ERPFLDELRR NEQDRLLVEL EQPLSSILAE MEFAGVKVDT KRLEQMGKEL AEQLGTVEQR IYELAGQEFN INSPKQLGVI LFEKLQLPVL KKTKTGYSTS ADVLEKLAPY HEIVENILHY RQLGKLQSTY IEGLLKVVRP ATKKVHTIFN QALTQTGRLS STEPNLQNIP IRLEEGRKIR QAFVPSESDW LIFAADYSQI ELRVLAHIAE DDNLMEAFRR DLDIHTKTAM DIFQVSEDEV TPNMRRQAKA VNFGIPYGIS DYGLAQNLNI SRKEAAEFIE RYFESFPGVK RYMENIVQEA KQKGYVTTLL HRRRYLPDIT SRNFNVRSFA ERMAMNTPIQ GSAADIIKKA MIDLNARLKE ERLQAHLLLQ VHDELILEAP KEEMERLCRL VPEVMEQAVT LRVPLKVDYH YGSTWYDAK //