NOP2B_ARATH
ID NOP2B_ARATH Reviewed; 671 AA.
AC Q8VYM6; Q9LDL2;
DT 26-FEB-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=26S rRNA (cytosine-C(5))-methyltransferase NOP2B {ECO:0000305};
DE EC=2.1.1.- {ECO:0000255|PROSITE-ProRule:PRU01023, ECO:0000269|PubMed:26268215};
DE AltName: Full=Nucleolar protein 2B {ECO:0000303|PubMed:26268215};
DE AltName: Full=tRNA methyltransferase 4d {ECO:0000303|PubMed:29268705};
DE Short=AtTRM4d {ECO:0000303|PubMed:29268705};
GN Name=NOP2B {ECO:0000303|PubMed:26268215};
GN Synonyms=TRM4d {ECO:0000303|PubMed:29268705};
GN OrderedLocusNames=At4g26600 {ECO:0000312|Araport:AT4G26600};
GN ORFNames=T15N24.50 {ECO:0000312|EMBL:CAB77061.1};
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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 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 [5]
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 probably
CC methylates the C(5) position of cytosine 1586 (m5C1586) in
CC mitochondrial 26S 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 (By similarity).
CC {ECO:0000250|UniProtKB:P46087, ECO:0000250|UniProtKB:Q9FG73,
CC ECO:0000269|PubMed:26268215}.
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:0000269|PubMed:26268215};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768}.
CC Nucleus, nucleolus {ECO:0000250|UniProtKB:P40991}.
CC -!- DISRUPTION PHENOTYPE: Normal levels of methylation at cytosine 2860 of
CC 25S rRNA, but slight reduction of mitochondrial 26S rRNA cytosine 1586
CC (m5C1586). {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=CAB77061.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB79515.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL078465; CAB77061.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161565; CAB79515.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE85225.1; -; Genomic_DNA.
DR EMBL; AY070425; AAL49920.1; -; mRNA.
DR EMBL; AY133836; AAM91770.1; -; mRNA.
DR PIR; T08926; T08926.
DR RefSeq; NP_194390.2; NM_118794.5.
DR AlphaFoldDB; Q8VYM6; -.
DR SMR; Q8VYM6; -.
DR STRING; 3702.AT4G26600.1; -.
DR PaxDb; Q8VYM6; -.
DR PRIDE; Q8VYM6; -.
DR ProteomicsDB; 185285; -.
DR EnsemblPlants; AT4G26600.1; AT4G26600.1; AT4G26600.
DR GeneID; 828767; -.
DR Gramene; AT4G26600.1; AT4G26600.1; AT4G26600.
DR KEGG; ath:AT4G26600; -.
DR Araport; AT4G26600; -.
DR TAIR; locus:2133832; AT4G26600.
DR eggNOG; KOG1122; Eukaryota.
DR HOGENOM; CLU_005316_3_1_1; -.
DR InParanoid; Q8VYM6; -.
DR PhylomeDB; Q8VYM6; -.
DR PRO; PR:Q8VYM6; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q8VYM6; baseline and differential.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008757; F:S-adenosylmethionine-dependent methyltransferase activity; IEA:InterPro.
DR GO; GO:0001510; P:RNA methylation; IEA:InterPro.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-KW.
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..671
FT /note="26S rRNA (cytosine-C(5))-methyltransferase NOP2B"
FT /id="PRO_0000448892"
FT REGION 1..188
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 550..671
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 28..35
FT /note="Nuclear localization signal 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 264..271
FT /note="Nuclear localization signal 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 594..601
FT /note="Nuclear localization signal 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 639..646
FT /note="Nuclear localization signal 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT COMPBIAS 7..29
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 41..58
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 59..129
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 136..188
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 550..568
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 596..610
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 620..671
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 477
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 350..356
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 374
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 401
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
FT BINDING 420
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01023"
SQ SEQUENCE 671 AA; 75543 MW; 6499B2821A217E10 CRC64;
MAALTRNKKK GSNSQTPPLN KQTKASPLKK AAKTQKPPLK KQRKCISEKK PLKKPEVSTD
EEEEEEENEQ SDEGSESGSD LFSDGDEEGN NDSDDDDDDD DDDDDDDEDA EPLAEDFLDG
SDNEEVTMGS DLDSDSGGSK LERKSRAIDR KRKKEVQDAD DEFKMNIKEK PDEFQLPTQK
ELEEEARRPP DLPSLQMRIR EIVRILSNFK DLKPKGDKHE RNDYVGQLKA DLSSYYGYNE
FLIGTLIEMF PVVELMELIE AFEKKRPTSI RTNTLKTRRR DLADILLNRG VNLDPLSKWS
KVGLIVYDSQ VPIGATPEYL AGFYMLQSAS SFLPVMALAP REKERVVDMA AAPGGKTTYV
AALMKNTGII YANEMKVPRL KSLSANLHRM GVTNTIVCNY DGRELTKVLG QSSVDRVLLD
APCSGTGVIS KDESVKTSKS ADDIKKFAHL QKQLILGAID LVDANSKTGG YIVYSTCSVM
IPENEAVIDY ALKNRDVKLV PCGLDFGRPG FSSFREHRFH PSLEKTRRFY PHVHNMDGFF
VAKLKKMSNA MQPSGNDEPA VTMEQAQVSS SDDDDEKAEA IEELEKPPVA SGQPKRESNT
KEDTNKRKNP RSKEIHKGKR NKNTKTESGN VEEPRKQKKK RSQWKNEIAQ AREEKRKTMR
ENAKETPKHR G
