ID   ROS1C_ORYSJ             Reviewed;        1858 AA.
AC   B8YIE8; A0A0P0WMX3; B9FPV3; Q0DHS4; Q65WT4;
DT   05-DEC-2018, integrated into UniProtKB/Swiss-Prot.
DT   05-DEC-2018, sequence version 2.
DT   03-AUG-2022, entry version 64.
DE   RecName: Full=Protein ROS1C {ECO:0000303|PubMed:22448681};
DE            EC=3.2.2.- {ECO:0000305};
DE   AltName: Full=DNA glycosylase 701 {ECO:0000303|PubMed:21896764};
DE   AltName: Full=Protein REPRESSOR OF SILENCING 1 homolog c {ECO:0000305};
GN   Name=ROS1C {ECO:0000303|PubMed:22448681};
GN   Synonyms=DNG701 {ECO:0000303|PubMed:21896764};
GN   OrderedLocusNames=Os05g0445900 {ECO:0000312|EMBL:BAF17599.1},
GN   LOC_Os05g37350 {ECO:0000305};
GN   ORFNames=OsJ_18723 {ECO:0000312|EMBL:EEE63898.1},
GN   P0615D12.11 {ECO:0000312|EMBL:AAU44279.1};
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 [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16261349; DOI=10.1007/s00438-005-0039-y;
RA   Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA   Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA   Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT   "A fine physical map of the rice chromosome 5.";
RL   Mol. Genet. Genomics 274:337-345(2005).
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).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [MRNA] OF 47-1858, FUNCTION, SUBCELLULAR LOCATION, AND
RP   DISRUPTION PHENOTYPE.
RX   PubMed=21896764; DOI=10.1073/pnas.1112704108;
RA   La H., Ding B., Mishra G.P., Zhou B., Yang H., Bellizzi Mdel R., Chen S.,
RA   Meyers B.C., Peng Z., Zhu J.K., Wang G.L.;
RT   "A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon
RT   Tos17 and promotes its transposition in rice.";
RL   Proc. Natl. Acad. Sci. U.S.A. 108:15498-15503(2011).
RN   [7]
RP   TISSUE SPECIFICITY.
RX   PubMed=22448681; DOI=10.1111/j.1365-313x.2012.05009.x;
RA   Ono A., Yamaguchi K., Fukada-Tanaka S., Terada R., Mitsui T., Iida S.;
RT   "A null mutation of ROS1a for DNA demethylation in rice is not
RT   transmittable to progeny.";
RL   Plant J. 71:564-574(2012).
CC   -!- FUNCTION: Bifunctional DNA glycosylase/lyase, which excises 5-
CC       methylcytosine (5-meC) and 5-hydroxymethylcytosine (5-hmeC), leaving an
CC       apyrimidinic (AP) site that is subsequently incised by the lyase
CC       activity (PubMed:21896764). Is responsible for the demethylation of
CC       methylated cytosine residues of Tos17 retrotransposon DNA
CC       (PubMed:21896764). Demethylation of Tos17 cytosine residues promotes
CC       its transposition (PubMed:21896764). May be involved in seed
CC       development (PubMed:21896764). {ECO:0000269|PubMed:21896764}.
CC   -!- COFACTOR:
CC       Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC         Evidence={ECO:0000250|UniProtKB:P0AB83};
CC       Note=Binds 1 [4Fe-4S] cluster. The cluster does not appear to play a
CC       role in catalysis, but is probably involved in the proper positioning
CC       of the enzyme along the DNA strand. {ECO:0000250|UniProtKB:P0AB83};
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:21896764}.
CC   -!- TISSUE SPECIFICITY: Expressed in pistils and immature seeds
CC       (PubMed:22448681). Expressed a low levels in roots, leaves and anthers
CC       (PubMed:22448681). {ECO:0000269|PubMed:22448681}.
CC   -!- DISRUPTION PHENOTYPE: Increased number of wrinkled seeds
CC       (PubMed:21896764). Hypermethylation of cytosine residues in the DNA
CC       sequence of Tos17 retrotransposons (PubMed:21896764).
CC       {ECO:0000269|PubMed:21896764}.
CC   -!- SIMILARITY: Belongs to the DNA glycosylase family. DEMETER subfamily.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAU44279.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAF17599.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAS94281.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAS94282.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AC137004; AAU44279.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008211; BAF17599.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014961; BAS94281.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014961; BAS94282.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CM000142; EEE63898.1; -; Genomic_DNA.
DR   EMBL; FJ536320; ACL80319.1; -; mRNA.
DR   RefSeq; XP_015640367.1; XM_015784881.1.
DR   AlphaFoldDB; B8YIE8; -.
DR   SMR; B8YIE8; -.
DR   STRING; 4530.OS05T0446000-01; -.
DR   GeneID; 4338940; -.
DR   KEGG; osa:4338940; -.
DR   eggNOG; ENOG502QQKH; Eukaryota.
DR   HOGENOM; CLU_008319_0_0_1; -.
DR   OrthoDB; 164157at2759; -.
DR   Proteomes; UP000000763; Chromosome 5.
DR   Proteomes; UP000007752; Chromosome 5.
DR   Proteomes; UP000059680; Chromosome 5.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:InterPro.
DR   GO; GO:0051747; F:cytosine C-5 DNA demethylase activity; IMP:CACAO.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0019104; F:DNA N-glycosylase activity; IEA:InterPro.
DR   GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006284; P:base-excision repair; IEA:InterPro.
DR   GO; GO:0080111; P:DNA demethylation; IDA:UniProtKB.
DR   CDD; cd00056; ENDO3c; 1.
DR   Gene3D; 1.10.1670.10; -; 1.
DR   InterPro; IPR044811; DME/ROS1.
DR   InterPro; IPR011257; DNA_glycosylase.
DR   InterPro; IPR003651; Endonuclease3_FeS-loop_motif.
DR   InterPro; IPR003265; HhH-GPD_domain.
DR   InterPro; IPR023170; HhH_base_excis_C.
DR   InterPro; IPR028925; RRM_DME.
DR   PANTHER; PTHR46213; PTHR46213; 1.
DR   Pfam; PF15628; RRM_DME; 1.
DR   SMART; SM00478; ENDO3c; 1.
DR   SMART; SM00525; FES; 1.
DR   SUPFAM; SSF48150; SSF48150; 1.
PE   2: Evidence at transcript level;
KW   DNA-binding; Hydrolase; Iron; Iron-sulfur; Lyase; Metal-binding; Nucleus;
KW   Reference proteome.
FT   CHAIN           1..1858
FT                   /note="Protein ROS1C"
FT                   /id="PRO_0000445980"
FT   REGION          347..416
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          1288..1309
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         1492
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250|UniProtKB:P0AB83"
FT   BINDING         1499
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250|UniProtKB:P0AB83"
FT   BINDING         1502
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250|UniProtKB:P0AB83"
FT   BINDING         1508
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000250|UniProtKB:P0AB83"
FT   CONFLICT        187
FT                   /note="Missing (in Ref. 5; EEE63898)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1858 AA;  207157 MW;  DF0838C45D95ADA8 CRC64;
     MAKDENPSYL HLIFLSSRIR VFILDPPLSL PLSHGQCELQ VVEEAAMDPS GLNLQGNPAE
     NQESWTSGVS VGRGTPNLGV GTAVAGRSCP SSTLFPGSSL SSTALLNTMH EGSFPQTALV
     AGSVSSADEQ HGAPPVRPSY NLPAGCTQVP ISILVFHRRL TGRGSRCRSP QSRSFMPAPA
     LSGVSEADGA YGPIPQSDFL SLRGPSEVFP GDMAMNHSEP ATSYGYNSEY APMHLQPNGL
     YTEASNTESE REASQLQQSA EAVICDSLSK LESAMEKIQG QNPQESSGLV AEGSADDNIH
     KYHQKAKRAR TQITHSDKID LPTQAVSACK EKTITQIEMQ IADAERTEAL KGEDAPAQKL
     KTRRRKHRPK VIREDRPAKK QMATTSEEKP LNQKPKRKYV RKNRNPSSLE KCAEPFSDHS
     ISRESRTTVR SSIASVRRRL QFEFGEHGVQ RDQSSMTNSW YQNQEKPVNA ESSLCSVTKS
     SVQVEHGQEL HMENSPEGLF FGINSKLNKI LDEYIHLPEA APKPSEQIPL AASGHVSEEL
     ARKQYDVRHT HDPDSTSYNI ERSGLITTKG HKKDLDLNYS NTNGFQMYCS ASLLPEMDST
     KGSMTKVSKM DKNKKRHYGG ESSLAGTQSS IIMRTAAEML AVYQACGIKK KRSARVRRNS
     FLSVMDLEKN TSQESTRLPR SCMEALYESS YIKFMTKKRS QKARLNSPNS IQPNIDQKNR
     FSSETVFSGG FNGLKRSEET FQKTLPQIPD DKRINLDIHC KVPVESSPNT STPPYMDYLQ
     GVTSKFRYFD LNTEQVHKTE MHLSQTMPSL SSLGATNYLP NALVPYVGGA VVPYQTQFHL
     VKKQRPRAKV DLDFETTRVW NLLMGKAADP VDGTDVDKER WWKQEREVFQ GRANSFIARM
     RLVQGDRRFS PWKGSVVDSV VGVFLTQNVA DHLSSSAYMA LAASFPTGSH GNCNDGIAGQ
     DNEEIISTSA VGDRGTFEFF YNGSRPDIGL NFEFSMACEK IHMEPKDNTT VNELTKGENY
     SLHCKESAGS LCDHETEIDH KAKSISDFSA VELTACMKNL HATQFQKEIS LSQSVVTSES
     ILQPGLPLSS GMDHARRNFV GSISDTASQQ VGSNFDDGKS LTGNDVTANE TEYHGIKAAA
     TNNYVVDEPG IPSGSSLYPF FSAIDCHQLD GRNDTHVSST SPNCSICSAS SNFKIGTIEE
     NSSLFMPFDA HLAQRNGNMI VDTNLSSALE STELPVKLLH CGKRSCYEAS EFQDHESLYA
     TGGVIPETAT KADDSTLKSG FASFNGLPDT AAQASKPKKS RTTSKKNSEN FDWDKLRRQA
     CGNYQMKERI FDRRDSVDWE AVRCADVQRI SHAIRERGMN NVLAERIQKF LNRLVTDHGS
     IDLEWLRDVP PDSAKDYLLS IRGLGLKSVE CVRLLTLHHL AFPVDTNVGR ICVRLGWVPI
     QPLPESLQLH LLELYPVLET IQKYLWPRLC KLDQQTLYEL HYQMITFGKV FCTKSKPNCN
     ACPMRSECRH FASAFASARL ALPSPQDKRL VNLSNQFAFH NGTMPTPNST PLPQLEGSIH
     ARDVHANNTN PIIEEPASPR EEECRELLEN DIEDFDEDTD EIPIIKLNME AFSQNLENCI
     KESNKDFQSD DITKALVAIS NEAASIPVPK LKNVHRLRTE HYVYELPDSH PLMQQLALDQ
     REPDDPSPYL LAIWTPDELK DTREAPKPCC NPQTEGGLCS NEMCHNCVSE RENQYRYVRG
     TVLVPCRTAM RGSFPLNGTY FQVNEVFADH SSSHNPINIP REQLWNLHRR MVYFGTSVPT
     IFKGLTTEEI QHCFWRGFVC VRGFNMETRA PRPLCPHFHL AASKLRRSSK KAATEQTH