NOP2A_ARATH
ID NOP2A_ARATH Reviewed; 682 AA.
AC Q9FG73; B9DFH3; Q8L8W4;
DT 26-FEB-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=25S rRNA (cytosine-C(5))-methyltransferase NOP2A {ECO:0000305};
DE EC=2.1.1.- {ECO:0000255|PROSITE-ProRule:PRU01023, ECO:0000269|PubMed:26268215};
DE AltName: Full=Nucleolar protein 2A {ECO:0000303|PubMed:26268215};
DE AltName: Full=Protein OLIGOCELLULA 2 {ECO:0000303|PubMed:19392710};
DE AltName: Full=tRNA methyltransferase 4c {ECO:0000303|PubMed:29268705};
DE Short=AtTRM4c {ECO:0000303|PubMed:29268705};
GN Name=NOP2A {ECO:0000303|PubMed:26268215};
GN Synonyms=OLI2 {ECO:0000303|PubMed:19392710},
GN TRM4c {ECO:0000303|PubMed:29268705};
GN OrderedLocusNames=At5g55920 {ECO:0000312|Araport:AT5G55920};
GN ORFNames=MYN21.3 {ECO:0000312|EMBL:BAB08657.1};
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;
RA Kaneko T., Katoh T., Asamizu E., Sato S., Nakamura Y., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. XI.";
RL Submitted (APR-1999) to the EMBL/GenBank/DDBJ databases.
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] OF 1-625.
RC STRAIN=cv. Columbia; TISSUE=Rosette leaf;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 529-682.
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19392710; DOI=10.1111/j.1365-313x.2009.03886.x;
RA Fujikura U., Horiguchi G., Ponce M.R., Micol J.L., Tsukaya H.;
RT "Coordination of cell proliferation and cell expansion mediated by
RT ribosome-related processes in the leaves of Arabidopsis thaliana.";
RL Plant J. 59:499-508(2009).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, AND CATALYTIC ACTIVITY.
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 [7]
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).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=cv. Columbia;
RX PubMed=29375609; DOI=10.3389/fpls.2017.02240;
RA Kojima K., Tamura J., Chiba H., Fukada K., Tsukaya H., Horiguchi G.;
RT "Two nucleolar proteins, GDP1 and OLI2, function as ribosome biogenesis
RT factors and are preferentially involved in promotion of leaf cell
RT proliferation without strongly affecting leaf adaxial-abaxial patterning in
RT Arabidopsis thaliana.";
RL Front. Plant Sci. 8:2240-2240(2017).
CC -!- FUNCTION: Involved in ribosomal large subunit assembly, required for
CC normal progression of rRNA processing (PubMed:26268215,
CC PubMed:29375609). S-adenosyl-L-methionine-dependent methyltransferase
CC that probably methylates the C(5) position of cytosine 2268 (m5C2268)
CC in nuclear 25S rRNA (PubMed:26268215). May play a role in the
CC regulation of the cell cycle and the increased nucleolar activity that
CC is associated with the cell proliferation (By similarity). Seems
CC involved in the regulation of cell proliferation in leaves
CC (PubMed:19392710, PubMed:29375609). {ECO:0000250|UniProtKB:P46087,
CC ECO:0000269|PubMed:19392710, ECO:0000269|PubMed:26268215,
CC ECO:0000269|PubMed:29375609}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a cytidine in 25S rRNA + S-adenosyl-L-methionine = a 5-
CC methylcytidine in 25S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:47780, Rhea:RHEA-COMP:11911, Rhea:RHEA-COMP:11912,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74483, ChEBI:CHEBI:82748;
CC Evidence={ECO:0000269|PubMed:26268215};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768}.
CC Nucleus, nucleolus {ECO:0000269|PubMed:29375609}.
CC -!- TISSUE SPECIFICITY: Strongly expressed in tissues with high cell
CC proliferation activity that have a high demand for ribosome production
CC such as guard cells, leaves primordia, root apical meristems and the
CC basal parts of lateral roots. {ECO:0000269|PubMed:29375609}.
CC -!- DISRUPTION PHENOTYPE: Moderate reduction in leaf cell number associated
CC with pointed leaves shape (PubMed:19392710). Defects in pre-rRNA
CC processing characterized by an increased accumulation of rRNA
CC intermediates containing 50-ETS, ITS1, or ITS2, with stronger negative
CC effect on ITS2-containing intermediates (PubMed:29375609). Higher
CC levels of 35S, 27SA, 27SB, P-A3, and 18SA3 rRNAs (PubMed:29375609).
CC Normal levels of methylation at cytosine 2860 of 25S rRNA, but slight
CC reduction of nuclear 25S rRNA cytosine 2268 (m5C2268)
CC (PubMed:26268215). Double mutants oli2 oli7 and oli2 oli5 have further
CC reduced cell number but exhibit also excessive postmitotic cell
CC enlargement in leaves (compensation phenotype) (PubMed:19392710). Plant
CC missing both OLI2 and GIF1/AN3 have a strong compensation phenotype
CC (PubMed:19392710). The double mutant gdp1 oli2 exhibit strong growth
CC defect due to a synergistically impaired cell proliferation in leaves
CC and enlarged cells (PubMed:29375609). {ECO:0000269|PubMed:19392710,
CC ECO:0000269|PubMed:26268215, ECO:0000269|PubMed:29375609}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RsmB/NOP family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM67083.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB026659; BAB08657.1; -; Genomic_DNA.
DR EMBL; CP002688; AED96699.1; -; Genomic_DNA.
DR EMBL; AK316770; BAH19490.1; -; mRNA.
DR EMBL; AY088769; AAM67083.1; ALT_INIT; mRNA.
DR RefSeq; NP_850927.1; NM_180596.2.
DR AlphaFoldDB; Q9FG73; -.
DR SMR; Q9FG73; -.
DR IntAct; Q9FG73; 3.
DR STRING; 3702.AT5G55920.1; -.
DR iPTMnet; Q9FG73; -.
DR PaxDb; Q9FG73; -.
DR PRIDE; Q9FG73; -.
DR ProteomicsDB; 181142; -.
DR EnsemblPlants; AT5G55920.1; AT5G55920.1; AT5G55920.
DR GeneID; 835690; -.
DR Gramene; AT5G55920.1; AT5G55920.1; AT5G55920.
DR KEGG; ath:AT5G55920; -.
DR Araport; AT5G55920; -.
DR TAIR; locus:2178393; AT5G55920.
DR eggNOG; KOG1122; Eukaryota.
DR HOGENOM; CLU_005316_3_1_1; -.
DR InParanoid; Q9FG73; -.
DR OMA; FRNIMTG; -.
DR OrthoDB; 1528896at2759; -.
DR PhylomeDB; Q9FG73; -.
DR PRO; PR:Q9FG73; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9FG73; baseline and differential.
DR GO; GO:0005730; C:nucleolus; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0009383; F:rRNA (cytosine-C5-)-methyltransferase activity; IBA:GO_Central.
DR GO; GO:0051301; P:cell division; IMP:TAIR.
DR GO; GO:0009965; P:leaf morphogenesis; IMP:TAIR.
DR GO; GO:0000470; P:maturation of LSU-rRNA; IBA:GO_Central.
DR GO; GO:0042127; P:regulation of cell population proliferation; IMP:UniProtKB.
DR GO; GO:0090069; P:regulation of ribosome biogenesis; IMP:UniProtKB.
DR GO; GO:0001510; P:RNA methylation; IBA:GO_Central.
DR GO; GO:0010015; P:root morphogenesis; IMP:TAIR.
DR GO; GO:0070475; P:rRNA base methylation; IBA:GO_Central.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR018314; Fmu/NOL1/Nop2p_CS.
DR InterPro; IPR031341; Methyltr_RsmF_N.
DR InterPro; IPR001678; MeTrfase_RsmB/NOP2.
DR InterPro; IPR011023; Nop2p.
DR InterPro; IPR023267; RCMT.
DR InterPro; IPR023273; RCMT_NOP2.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR PANTHER; PTHR22807; PTHR22807; 1.
DR Pfam; PF01189; Methyltr_RsmB-F; 1.
DR Pfam; PF17125; Methyltr_RsmF_N; 1.
DR PRINTS; PR02008; RCMTFAMILY.
DR PRINTS; PR02012; RCMTNOP2.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR00446; nop2p; 1.
DR PROSITE; PS01153; NOL1_NOP2_SUN; 1.
DR PROSITE; PS51686; SAM_MT_RSMB_NOP; 1.
PE 1: Evidence at protein level;
KW Methyltransferase; Nucleus; Reference proteome; Ribosome biogenesis;
KW RNA-binding; rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..682
FT /note="25S rRNA (cytosine-C(5))-methyltransferase NOP2A"
FT /id="PRO_0000448891"
FT REGION 1..155
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 567..682
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 38..45
FT /note="Nuclear localization signal 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 616..623
FT /note="Nuclear localization signal 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 635..642
FT /note="Nuclear localization signal 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 655..662
FT /note="Nuclear localization signal 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 10..42
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 62..151
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 576..599
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 600..651
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 658..682
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 494
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 367..373
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 391
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 418
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 437
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT CONFLICT 657
FT /note="R -> W (in Ref. 4; AAM67083)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 682 AA; 76776 MW; 2EFAFFA109474BCD CRC64;
MPALTRNKKK AATKSITPPT KQLTKSKTPP MKPQTSMLKK GAKSQNKPPL KKQKKEVVEE
EPLEDYEVTD DSDEDDEVSD GSDEDDISPA VESEEIDESD DGENGSNQLF SDDEEENDEE
TLGDDFLEGS GDEDEEGSLD ADSDADSDDD DIVAKSDAID RDLAMQKKDA AAELEDFIKQ
DDVHDEEPEH DAFRLPTEEE LEEEARGPPD LPLLKTRIEE IVRALKNFKA FRPKDTTRKA
CVEQLKADLG SYYGYNSFLI GTLVEMFPPG ELMELIEAFE KQRPTSIRTN TLKTRRRDLA
DVLLNRGVNL DPLSKWSKVG LVIYDSQVPI GATPEYLAGY YMLQGASSFL PVMALAPREN
ERIVDVAAAP GGKTTYIAAL MKNTGLIYAN EMKVPRLKSL TANLHRMGVT NTIVCNYDGR
ELPKVLGQNT VDRVLLDAPC SGTGIISKDE SVKITKTMDE IKKFAHLQKQ LLLAAIDMVD
ANSKTGGYIV YSTCSIMVTE NEAVIDYALK KRDVKLVTCG LDFGRKGFTR FREHRFQPSL
DKTRRFYPHV HNMDGFFVAK LKKMSNVKQS SEEGDDDAVE TVEQAEVSSD DDDEAEAIEE
TEKPSVPVRQ PKERKEKKNK EKLAKSKEDK RGKKDKKSKS ENVEEPSKPR KQKKKRREWK
NEIAQAREEK RIAMREKAKE EK
