DPOLL_ORYSJ
ID DPOLL_ORYSJ Reviewed; 549 AA.
AC Q67VC8; Q0DDB2; Q6L9M0;
DT 02-NOV-2016, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 93.
DE RecName: Full=DNA polymerase lambda;
DE Short=OsPolL {ECO:0000303|PubMed:15206945};
DE Short=Pol Lambda {ECO:0000305};
DE EC=2.7.7.7 {ECO:0000269|PubMed:15206945};
DE EC=4.2.99.- {ECO:0000305};
GN Name=POLL {ECO:0000305};
GN OrderedLocusNames=Os06g0237200 {ECO:0000312|EMBL:BAS96965.1},
GN LOC_Os06g13020 {ECO:0000305};
GN ORFNames=OSJNBa0068B06.5 {ECO:0000312|EMBL:BAD18976.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP INTERACTION WITH PCNA, TISSUE SPECIFICITY, INDUCTION, AND MUTAGENESIS OF
RP ASP-397 AND ASP-399.
RC STRAIN=cv. Nipponbare;
RX PubMed=15206945; DOI=10.1111/j.1432-1033.2004.04214.x;
RA Uchiyama Y., Kimura S., Yamamoto T., Ishibashi T., Sakaguchi K.;
RT "Plant DNA polymerase lambda, a DNA repair enzyme that functions in plant
RT meristematic and meiotic tissues.";
RL Eur. J. Biochem. 271:2799-2807(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
CC -!- FUNCTION: Repair polymerase involved in base excision repair (BER) and
CC responsible for repair of lesions that give rise to abasic (AP) sites
CC in DNA. Has both DNA polymerase and terminal transferase activities.
CC Has a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity.
CC {ECO:0000269|PubMed:15206945}.
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:15206945};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:15206945};
CC -!- SUBUNIT: Interacts with PCNA. {ECO:0000269|PubMed:15206945}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in proliferating tissues. Expressed in
CC roots, root apex, young leaves, shoot apical meristem (SAM), flag
CC leaves and panicles. {ECO:0000269|PubMed:15206945}.
CC -!- INDUCTION: By UV treatment and methyl methanesulfonate (MMS).
CC {ECO:0000269|PubMed:15206945}.
CC -!- SIMILARITY: Belongs to the DNA polymerase type-X family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAF19161.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAS96965.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB099525; BAD18976.1; -; mRNA.
DR EMBL; AP004995; BAD37891.1; -; Genomic_DNA.
DR EMBL; AP008212; BAF19161.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP014962; BAS96965.1; ALT_SEQ; Genomic_DNA.
DR RefSeq; XP_015643819.1; XM_015788333.1.
DR AlphaFoldDB; Q67VC8; -.
DR SMR; Q67VC8; -.
DR STRING; 4530.OS06T0237200-00; -.
DR PRIDE; Q67VC8; -.
DR GeneID; 4340604; -.
DR KEGG; osa:4340604; -.
DR eggNOG; KOG2534; Eukaryota.
DR InParanoid; Q67VC8; -.
DR OrthoDB; 1328151at2759; -.
DR Proteomes; UP000000763; Chromosome 6.
DR Proteomes; UP000059680; Chromosome 6.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0051575; F:5'-deoxyribose-5-phosphate lyase activity; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0097510; P:base-excision repair, AP site formation via deaminated base removal; IDA:UniProtKB.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IBA:GO_Central.
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 Gene3D; 3.40.50.10190; -; 1.
DR InterPro; IPR001357; BRCT_dom.
DR InterPro; IPR036420; BRCT_dom_sf.
DR InterPro; IPR002054; DNA-dir_DNA_pol_X.
DR InterPro; IPR019843; DNA_pol-X_BS.
DR InterPro; IPR010996; DNA_pol_b-like_N.
DR InterPro; IPR028207; DNA_pol_B_palm_palm.
DR InterPro; IPR018944; DNA_pol_lambd_fingers_domain.
DR InterPro; IPR027421; DNA_pol_lamdba_lyase_dom_sf.
DR InterPro; IPR037160; DNA_Pol_thumb_sf.
DR InterPro; IPR022312; DNA_pol_X.
DR InterPro; IPR002008; DNA_pol_X_beta-like.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR029398; PolB_thumb.
DR PANTHER; PTHR11276; PTHR11276; 1.
DR Pfam; PF14792; DNA_pol_B_palm; 1.
DR Pfam; PF14791; DNA_pol_B_thumb; 1.
DR Pfam; PF10391; DNA_pol_lambd_f; 1.
DR Pfam; PF14716; HHH_8; 1.
DR PRINTS; PR00869; DNAPOLX.
DR PRINTS; PR00870; DNAPOLXBETA.
DR SMART; SM00483; POLXc; 1.
DR SUPFAM; SSF47802; SSF47802; 1.
DR SUPFAM; SSF52113; SSF52113; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
DR PROSITE; PS50172; BRCT; 1.
DR PROSITE; PS00522; DNA_POLYMERASE_X; 1.
PE 1: Evidence at protein level;
KW DNA damage; DNA repair; DNA replication; DNA synthesis; DNA-binding;
KW DNA-directed DNA polymerase; Lyase; Manganese; Metal-binding;
KW Nucleotidyltransferase; Nucleus; Reference proteome; Transferase.
FT CHAIN 1..549
FT /note="DNA polymerase lambda"
FT /id="PRO_0000438213"
FT DOMAIN 17..116
FT /note="BRCT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT REGION 126..197
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 233..247
FT /note="DNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP5"
FT REGION 315..318
FT /note="DNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP5"
FT REGION 390..399
FT /note="Involved in primer binding"
FT /evidence="ECO:0000250"
FT REGION 438..479
FT /note="DNA-binding"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP5"
FT COMPBIAS 145..171
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 176..197
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 280
FT /evidence="ECO:0000305"
FT BINDING 356
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP5"
FT BINDING 387..390
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP5"
FT BINDING 396..399
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP5"
FT BINDING 397
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP5"
FT BINDING 399
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP5"
FT BINDING 464
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP5"
FT BINDING 487
FT /ligand="dCTP"
FT /ligand_id="ChEBI:CHEBI:61481"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP5"
FT MUTAGEN 397
FT /note="D->A: Loss of polymerase activity; when associated
FT with A-399."
FT /evidence="ECO:0000269|PubMed:15206945"
FT MUTAGEN 399
FT /note="D->A: Loss of polymerase activity; when associated
FT with A-397."
FT /evidence="ECO:0000269|PubMed:15206945"
FT CONFLICT 11
FT /note="A -> AAAA (in Ref. 1; BAD18976)"
FT /evidence="ECO:0000305"
FT CONFLICT 423
FT /note="G -> D (in Ref. 1; BAD18976)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 549 AA; 60628 MW; CBDEBE99CA6BEF46 CRC64;
MAPKRKPPAR AAAAKLDPDG MFRGVSAFVV PHAVQSRRLE VWKQRLAQMG GRVQEKLAAK
GGGGAVTHVL AADAKALLRE LDAAWLHRFR GSVVSFEWLE ECLKSGERLP EHKFAINYEE
EFKPKKEGGA AGSGVLQSAK RSKISSDGPE NRKETAGGNR ESRDAIAHPN EDSDVVKGPS
TCTSSQSASG DSKETIASQN AFKAEEASSG ESSTYAPPDL NRNITEIFGK LINIYRALGD
DRRSFSYYKA IPVIEKLPFK IESADQVKDL PAIGKSLKDH INEIVNTGKL SKLEHFENDE
KVRTVSLFGE VWGVGPATAL KLYDKGHRTL DDLQKDDSLT SAQRIGLKFF DDIKQRIPRH
EVSEMEKLLQ EVGTDILPGV IIVCGGSYRR GKSSCGDMDI IITHPDGESH VGFLPKFVQR
LKGINFLRED LIFSIHSIEG TDCGVDTYFG LCTYPGRELR HRIDLKVYPR NRHAFGLLAW
TGNDVLNRRL RILADSKGYI LDDTGLYLAT PGSGGKRGGR SDAIINCDTE KDVFDTLGFP
WLEPHERNL
