ID C5Y6L0_SORBI Unreviewed; 1099 AA.
AC C5Y6L0;
DT 01-SEP-2009, integrated into UniProtKB/TrEMBL.
DT 01-SEP-2009, sequence version 1.
DT 27-MAR-2024, entry version 85.
DE RecName: Full=DNA polymerase {ECO:0000256|RuleBase:RU000442};
DE EC=2.7.7.7 {ECO:0000256|RuleBase:RU000442};
GN ORFNames=SORBI_3005G066900 {ECO:0000313|EMBL:EES09438.1};
OS Sorghum bicolor (Sorghum) (Sorghum vulgare).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade;
OC Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum.
OX NCBI_TaxID=4558 {ECO:0000313|EMBL:EES09438.1, ECO:0000313|Proteomes:UP000000768};
RN [1] {ECO:0000313|EMBL:EES09438.1, ECO:0000313|Proteomes:UP000000768}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. BTx623 {ECO:0000313|Proteomes:UP000000768};
RX PubMed=19189423; DOI=10.1038/nature07723;
RA Paterson A.H., Bowers J.E., Bruggmann R., Dubchak I., Grimwood J.,
RA Gundlach H., Haberer G., Hellsten U., Mitros T., Poliakov A., Schmutz J.,
RA Spannagl M., Tang H., Wang X., Wicker T., Bharti A.K., Chapman J.,
RA Feltus F.A., Gowik U., Grigoriev I.V., Lyons E., Maher C.A., Martis M.,
RA Narechania A., Otillar R.P., Penning B.W., Salamov A.A., Wang Y., Zhang L.,
RA Carpita N.C., Freeling M., Gingle A.R., Hash C.T., Keller B., Klein P.,
RA Kresovich S., McCann M.C., Ming R., Peterson D.G., Mehboob-ur-Rahman,
RA Ware D., Westhoff P., Mayer K.F., Messing J., Rokhsar D.S.;
RT "The Sorghum bicolor genome and the diversification of grasses.";
RL Nature 457:551-556(2009).
RN [2] {ECO:0000313|Proteomes:UP000000768}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. BTx623 {ECO:0000313|Proteomes:UP000000768};
RX PubMed=29161754; DOI=10.1111/tpj.13781;
RA McCormick R.F., Truong S.K., Sreedasyam A., Jenkins J., Shu S., Sims D.,
RA Kennedy M., Amirebrahimi M., Weers B.D., McKinley B., Mattison A.,
RA Morishige D.T., Grimwood J., Schmutz J., Mullet J.E.;
RT "The Sorghum bicolor reference genome: improved assembly, gene annotations,
RT a transcriptome atlas, and signatures of genome organization.";
RL Plant J. 93:338-354(2018).
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:RU000442};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|ARBA:ARBA00001966,
CC ECO:0000256|RuleBase:RU000442};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|RuleBase:RU000442}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-B family.
CC {ECO:0000256|ARBA:ARBA00005755, ECO:0000256|RuleBase:RU000442}.
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DR EMBL; CM000764; EES09438.1; -; Genomic_DNA.
DR RefSeq; XP_002450450.1; XM_002450405.1.
DR AlphaFoldDB; C5Y6L0; -.
DR STRING; 4558.C5Y6L0; -.
DR EnsemblPlants; EES09438; EES09438; SORBI_3005G066900.
DR GeneID; 8072800; -.
DR Gramene; EES09438; EES09438; SORBI_3005G066900.
DR KEGG; sbi:8072800; -.
DR eggNOG; KOG0969; Eukaryota.
DR HOGENOM; CLU_000203_2_0_1; -.
DR InParanoid; C5Y6L0; -.
DR OMA; CNNCRPR; -.
DR OrthoDB; 211439at2759; -.
DR Proteomes; UP000000768; Chromosome 5.
DR GO; GO:0043625; C:delta DNA polymerase complex; IBA:GO_Central.
DR GO; GO:0008296; F:3'-5'-DNA exonuclease activity; IBA:GO_Central.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
DR GO; GO:0006287; P:base-excision repair, gap-filling; IBA:GO_Central.
DR GO; GO:0045004; P:DNA replication proofreading; IBA:GO_Central.
DR GO; GO:0006261; P:DNA-templated DNA replication; IBA:GO_Central.
DR GO; GO:0006297; P:nucleotide-excision repair, DNA gap filling; IBA:GO_Central.
DR CDD; cd05777; DNA_polB_delta_exo; 1.
DR CDD; cd05533; POLBc_delta; 1.
DR Gene3D; 1.10.132.60; DNA polymerase family B, C-terminal domain; 1.
DR Gene3D; 3.30.342.10; DNA Polymerase, chain B, domain 1; 1.
DR Gene3D; 1.10.287.690; Helix hairpin bin; 1.
DR Gene3D; 3.90.1600.10; Palm domain of DNA polymerase; 1.
DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 1.
DR InterPro; IPR006172; DNA-dir_DNA_pol_B.
DR InterPro; IPR017964; DNA-dir_DNA_pol_B_CS.
DR InterPro; IPR006133; DNA-dir_DNA_pol_B_exonuc.
DR InterPro; IPR006134; DNA-dir_DNA_pol_B_multi_dom.
DR InterPro; IPR043502; DNA/RNA_pol_sf.
DR InterPro; IPR042087; DNA_pol_B_thumb.
DR InterPro; IPR023211; DNA_pol_palm_dom_sf.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR InterPro; IPR025687; Znf-C4pol.
DR NCBIfam; TIGR00592; pol2; 1.
DR PANTHER; PTHR10322; DNA POLYMERASE CATALYTIC SUBUNIT; 1.
DR PANTHER; PTHR10322:SF23; DNA POLYMERASE DELTA CATALYTIC SUBUNIT; 1.
DR Pfam; PF00136; DNA_pol_B; 1.
DR Pfam; PF03104; DNA_pol_B_exo1; 1.
DR Pfam; PF14260; zf-C4pol; 1.
DR PRINTS; PR00106; DNAPOLB.
DR SMART; SM00486; POLBc; 1.
DR SUPFAM; SSF56672; DNA/RNA polymerases; 1.
DR SUPFAM; SSF53098; Ribonuclease H-like; 1.
DR PROSITE; PS00116; DNA_POLYMERASE_B; 1.
PE 3: Inferred from homology;
KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|RuleBase:RU000442};
KW DNA replication {ECO:0000256|RuleBase:RU000442};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|RuleBase:RU000442};
KW DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022932,
KW ECO:0000256|RuleBase:RU000442};
KW Exonuclease {ECO:0000256|ARBA:ARBA00022839};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|RuleBase:RU000442};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|RuleBase:RU000442};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW ECO:0000256|RuleBase:RU000442}; Nuclease {ECO:0000256|ARBA:ARBA00022722};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695,
KW ECO:0000256|RuleBase:RU000442};
KW Nucleus {ECO:0000256|ARBA:ARBA00023242, ECO:0000256|RuleBase:RU000442};
KW Reference proteome {ECO:0000313|Proteomes:UP000000768};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|RuleBase:RU000442};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|RuleBase:RU000442};
KW Zinc-finger {ECO:0000256|RuleBase:RU000442}.
FT DOMAIN 185..475
FT /note="DNA-directed DNA polymerase family B exonuclease"
FT /evidence="ECO:0000259|Pfam:PF03104"
FT DOMAIN 539..972
FT /note="DNA-directed DNA polymerase family B
FT multifunctional"
FT /evidence="ECO:0000259|Pfam:PF00136"
FT DOMAIN 1009..1080
FT /note="C4-type zinc-finger of DNA polymerase delta"
FT /evidence="ECO:0000259|Pfam:PF14260"
FT REGION 1..42
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1099 AA; 123052 MW; 1196CF57D7F1D758 CRC64;
MSSGGRGGKR RGPPPPAPSG AAAKRANPSP GMPQPPPPAA AEEDMMDEDV FLDESILAED
EAALLMLQRD EALASRLARW KRPALPSDLA AGCSRAVAFQ QLEIDYVIGE SHKELLPNSS
GSAAILRIFG VTREGHSICC QVHGFEPYFY IGCPSGMGPD DISRFHQTLE GRMKESNRSS
NVPRFVKRVE LVQKQTIMHY QTQESQPFLK IVVALPTMVA SCRGILERGI MIEGLGSKSF
LTYESNILFA LRFMIDCNIV GGNWIELPAG KYRKAARLMS YCQLELDCLY SDLVSHAAEG
EYSKMAPFRI LSFDIECAGR KGHFPEPTHD PVIQIANLVT HQGEGQPFVQ NVMTLKSCSP
IVGVDVRSFD TERDILLAWR DFIREVDPDI IIGYNICKFD MPYLIERAEV LKIAEFPILG
RIRNSRVRVR DTTFSSRQYG VRESKDVTIE GRVQFDLLQA MQRDYKLSSY SLNSVSAHFL
GEQKEDVHHS IISDLQNGNS ETRRRLAVYC LKDAYLPQRL LDKLMYIYNY VEMARVTGVP
ISFLLSRGQS IKVLSQLLRK AKQKNLVIPN IKGQGSGQDT FEGATVLEAR AGFYEKPIAT
LDFASLYPSI MMAYNLCYCT LVPPEDARKL NLPPESINKT PSGEIFVKPE LQKGILPEIL
EELLAARKRA KADLKEAKDP LERAVLDGRQ LALKISANSV YGFTGATVGQ LPCLEISSSV
TSYGRQMIEH TKKLVEDKFT TVGGYEHNAE VIYGDTDSVM VQFGVSTVQD AMKLGREAAD
YISGTFTKPI KLEFEKVYFP YLLISKKRYA GLYWTNPEKF DKMDAKGIET VRRDNCLLVK
NLVTECLHKI LVDRDVPGAV QYVKNTISDL LMNRVDLSLL VITKGLTKTG EDYAVKAAHV
ELAERMRKRD PATAPTVGDR VPYVIIKAAK GAKAYEKSED PIYVLDNNIP IDPQYYLENQ
ISKPLLRIFE PILKNASKEL LHGSHTRSVS ISTPSNSGIM KFAKKQLTCL GCKAVISGAS
QTLCSHCKGR EAELYCKTVA NVSDLEMLFG RLWTQCQECQ GSLHQDVLCT SRDCPIFYRR
RKAQKDMAEA RLQLDRWDF
//