NOP2C_ARATH
ID NOP2C_ARATH Reviewed; 599 AA.
AC Q84MA1; Q9SHJ9; Q9SHK0;
DT 26-FEB-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=rRNA (cytosine-C(5))-methyltransferase NOP2C {ECO:0000305};
DE EC=2.1.1.- {ECO:0000255|PROSITE-ProRule:PRU01023};
DE AltName: Full=Nucleolar protein 2C {ECO:0000303|PubMed:26268215};
DE AltName: Full=tRNA methyltransferase 4f {ECO:0000303|PubMed:29268705};
DE Short=AtTRM4f {ECO:0000303|PubMed:29268705};
GN Name=NOP2C {ECO:0000303|PubMed:26268215};
GN Synonyms=TRM4f {ECO:0000303|PubMed:29268705};
GN OrderedLocusNames=At1g06560 {ECO:0000312|Araport:AT1G06560};
GN ORFNames=F12K11.10 {ECO:0000312|EMBL:AAF24826.1},
GN F12K11.11 {ECO:0000312|EMBL:AAF24825.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=26268215; DOI=10.1186/s12870-015-0580-8;
RA Burgess A.L., David R., Searle I.R.;
RT "Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae.";
RL BMC Plant Biol. 15:199-199(2015).
RN [6]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=29268705; DOI=10.1186/s12870-017-1206-0;
RA Wang Y., Pang C., Li X., Hu Z., Lv Z., Zheng B., Chen P.;
RT "Identification of tRNA nucleoside modification genes critical for stress
RT response and development in rice and Arabidopsis.";
RL BMC Plant Biol. 17:261-261(2017).
CC -!- FUNCTION: Involved in ribosomal large subunit assembly (By similarity).
CC S-adenosyl-L-methionine-dependent methyltransferase that may methylates
CC the C(5) position of cytosine in rRNA (By similarity). May play a role
CC in the regulation of the cell cycle and the increased nucleolar
CC activity that is associated with the cell proliferation (By
CC similarity). Seems involved in the regulation of cell proliferation (By
CC similarity). {ECO:0000250|UniProtKB:P46087,
CC ECO:0000250|UniProtKB:Q9FG73}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a cytidine in rRNA + S-adenosyl-L-methionine = a 5-
CC methylcytidine in rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:61484, Rhea:RHEA-COMP:15836, Rhea:RHEA-COMP:15837,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000250|UniProtKB:Q9FG73};
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:P40991}.
CC -!- DISRUPTION PHENOTYPE: Normal levels of methylation at cytosine 2860 of
CC 25S rRNA. {ECO:0000269|PubMed:26268215}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF24825.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAF24826.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC007592; AAF24825.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC007592; AAF24826.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE28005.1; -; Genomic_DNA.
DR EMBL; BT006450; AAP21258.1; -; mRNA.
DR EMBL; AK227718; BAE99704.1; -; mRNA.
DR PIR; A86201; A86201.
DR RefSeq; NP_172143.3; NM_100535.4.
DR AlphaFoldDB; Q84MA1; -.
DR SMR; Q84MA1; -.
DR STRING; 3702.AT1G06560.1; -.
DR PaxDb; Q84MA1; -.
DR PRIDE; Q84MA1; -.
DR ProteomicsDB; 185604; -.
DR EnsemblPlants; AT1G06560.1; AT1G06560.1; AT1G06560.
DR GeneID; 837167; -.
DR Gramene; AT1G06560.1; AT1G06560.1; AT1G06560.
DR KEGG; ath:AT1G06560; -.
DR Araport; AT1G06560; -.
DR TAIR; locus:2009170; AT1G06560.
DR eggNOG; KOG1122; Eukaryota.
DR HOGENOM; CLU_005316_1_0_1; -.
DR InParanoid; Q84MA1; -.
DR OMA; VCVAVEQ; -.
DR OrthoDB; 1040075at2759; -.
DR PhylomeDB; Q84MA1; -.
DR PRO; PR:Q84MA1; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q84MA1; baseline and differential.
DR GO; GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0001510; P:RNA methylation; IBA:GO_Central.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 2.30.130.10; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR018314; Fmu/NOL1/Nop2p_CS.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR002478; PUA.
DR InterPro; IPR015947; PUA-like_sf.
DR InterPro; IPR036974; PUA_sf.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR22807; PTHR22807; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 2.
DR Pfam; PF01472; PUA; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR SMART; SM00359; PUA; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR SUPFAM; SSF88697; SSF88697; 1.
DR PROSITE; PS01153; NOL1_NOP2_SUN; 1.
DR PROSITE; PS50890; PUA; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 2: Evidence at transcript level;
KW Methyltransferase; Nucleus; Reference proteome; Ribosome biogenesis;
KW RNA-binding; rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..599
FT /note="rRNA (cytosine-C(5))-methyltransferase NOP2C"
FT /id="PRO_0000448893"
FT DOMAIN 158..265
FT /note="PUA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00161"
FT REGION 372..454
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 372..396
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 397..411
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 516
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 304..310
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 328
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 355
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 465
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
SQ SEQUENCE 599 AA; 65513 MW; F2DCB8D28502CBF7 CRC64;
MSKARVLLKP SSLTTCLTRA KAFFSSVSQS RSISHQMEMG PSDSERYCYD PVLRWNPEVE
DYFTKAYGPD HFARISKALT RPSSYSCIRV NTVKTTSDAV IEKLTKILND SEEGLKLVQP
DGSSPVTKCQ IPGLDYVVFV NGSGPHKIEY DSGLENPPKE VLVSRKCAEA VLRGAQVYVP
GVLACTAHVE KGDAVAVCVA MEQPGDEGDW SVNMTRGTTL QGLPTDPYYR ERSGLYIGMG
TAMLSRAGMF RVPNGIAVDL NHRVFRLPSL HNILEGEIFL QNLPSIIVAH ALDPQKGERI
LDMCAAPGGK TTAIAILMND EGEIVAADRS HNKVLVVQNL SAEMGFTCIT TCKLDALKSV
CLPTTLNEST ILINGDNSSS MTSHSELSSN EEMTSVTSRR SEADKSCEKN DSTEQPNGGD
NVSQAYIRKN KGRLKNGRGR TQCQGGRAGK SQGFPPNSFD RVLLDAPCSA LGLRPRLFAG
LETVVSLRNH GWYQRKMLDQ AVQLVRVGGI LVYSTCTINP SENEAVVRYA LDKYRFLSLA
PQHPRIGGPG LVGRCEFPDG YIEEWLKPGE EELVQKFDPS SELDTIGFFI AKFSVGPKD
