TRM13_ORYSJ
ID TRM13_ORYSJ Reviewed; 250 AA.
AC Q10B19; Q75LH5; Q7Y148;
DT 30-AUG-2017, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=tRNA:m(4)X modification enzyme TRM13 {ECO:0000305};
DE EC=2.1.1.225 {ECO:0000305|PubMed:28369540};
DE AltName: Full=tRNA methylase 13 {ECO:0000305};
DE Short=OsTRM13 {ECO:0000303|PubMed:28369540};
GN Name=TRM13 {ECO:0000303|PubMed:28369540};
GN OrderedLocusNames=Os03g0833200 {ECO:0000312|EMBL:BAH92428.1},
GN LOC_Os03g61750 {ECO:0000312|EMBL:ABF99727.1};
GN ORFNames=OSJNBa0078D06.36 {ECO:0000312|EMBL:AAP46236.1},
GN OSJNBa0096I06.32 {ECO:0000312|EMBL:AAR88577.1};
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=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(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 MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION, AND INDUCTION.
RX PubMed=28369540; DOI=10.1093/jxb/erx061;
RA Wang Y., Li D., Gao J., Li X., Zhang R., Jin X., Hu Z., Zheng B.,
RA Persson S., Chen P.;
RT "The 2'-O-methyladenosine nucleoside modification gene OsTRM13 positively
RT regulates salt stress tolerance in rice.";
RL J. Exp. Bot. 68:1479-1491(2017).
CC -!- FUNCTION: tRNA methylase that catalyzes 2'-O-methyladenosine (Am)
CC nucleoside formation on tRNA(Gly)(GCC) in vitro. May 2'-O-methylate
CC cytidine(4) in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine(4) in
CC tRNA(His) (PubMed:28369540). Involved in salt stress tolerance
CC (PubMed:28369540). {ECO:0000269|PubMed:28369540}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(4) in tRNA(Pro) + S-adenosyl-L-methionine = 2'-O-
CC methylcytidine(4) in tRNA(Pro) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:32767, Rhea:RHEA-COMP:10397, Rhea:RHEA-COMP:10398,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.225;
CC Evidence={ECO:0000305|PubMed:28369540};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cytidine(4) in tRNA(Gly)(GCC) + S-adenosyl-L-methionine = 2'-
CC O-methylcytidine(4) in tRNA(Gly)(GCC) + H(+) + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:43192, Rhea:RHEA-COMP:10399, Rhea:RHEA-
CC COMP:10400, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74495, ChEBI:CHEBI:82748; EC=2.1.1.225;
CC Evidence={ECO:0000305|PubMed:28369540};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(4) in tRNA(His) + S-adenosyl-L-methionine = 2'-O-
CC methyladenosine(4) in tRNA(His) + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:43196, Rhea:RHEA-COMP:10401, Rhea:RHEA-COMP:10402,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74477; EC=2.1.1.225;
CC Evidence={ECO:0000305|PubMed:28369540};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:28369540}. Cytoplasm
CC {ECO:0000305|PubMed:28369540}.
CC -!- INDUCTION: Induced by salt stress and abscisic acid treatment.
CC {ECO:0000269|PubMed:28369540}.
CC -!- MISCELLANEOUS: Seedlings subjected to salt stress and abscisic acid
CC (ABA) treatment exhibit a dramatic increase of 2'-O-methyladenosine
CC (Am) nucleoside (PubMed:28369540). Plants over-expressing TRM13 show
CC improved salt stress tolerance, and plant silencing TRM13 display
CC decreased stress tolerance (PubMed:28369540).
CC {ECO:0000269|PubMed:28369540}.
CC -!- SIMILARITY: Belongs to the methyltransferase TRM13 family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAP46236.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=AAR88577.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC092557; AAR88577.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AC133339; AAP46236.1; ALT_SEQ; Genomic_DNA.
DR EMBL; DP000009; ABF99727.1; -; Genomic_DNA.
DR EMBL; AP008209; BAH92428.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS87224.1; -; Genomic_DNA.
DR EMBL; AK102870; BAG95757.1; -; mRNA.
DR AlphaFoldDB; Q10B19; -.
DR STRING; 4530.OS03T0833200-01; -.
DR PaxDb; Q10B19; -.
DR PRIDE; Q10B19; -.
DR EnsemblPlants; Os03t0833200-01; Os03t0833200-01; Os03g0833200.
DR Gramene; Os03t0833200-01; Os03t0833200-01; Os03g0833200.
DR eggNOG; KOG2811; Eukaryota.
DR HOGENOM; CLU_106946_0_0_1; -.
DR InParanoid; Q10B19; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0106050; F:tRNA 2'-O-methyltransferase activity; IEA:InterPro.
DR GO; GO:0008175; F:tRNA methyltransferase activity; IDA:UniProtKB.
DR GO; GO:0009651; P:response to salt stress; IMP:UniProtKB.
DR GO; GO:0030488; P:tRNA methylation; IDA:UniProtKB.
DR InterPro; IPR007871; Methyltransferase_TRM13.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR039044; Trm13.
DR InterPro; IPR022776; TRM13/UPF0224_CHHC_Znf_dom.
DR InterPro; IPR021721; Znf_CCCH-type_TRM13.
DR PANTHER; PTHR12998; PTHR12998; 1.
DR Pfam; PF05206; TRM13; 1.
DR Pfam; PF11722; zf-TRM13_CCCH; 1.
DR Pfam; PF05253; zf-U11-48K; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR PROSITE; PS51800; ZF_CHHC_U11_48K; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Metal-binding; Methyltransferase; Nucleus; Reference proteome;
KW S-adenosyl-L-methionine; Stress response; Transferase; tRNA processing;
KW Zinc; Zinc-finger.
FT CHAIN 1..250
FT /note="tRNA:m(4)X modification enzyme TRM13"
FT /id="PRO_0000441221"
FT ZN_FING 62..89
FT /note="CHHC U11-48K-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT REGION 1..20
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 65
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 71
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 81
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
FT BINDING 85
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01141"
SQ SEQUENCE 250 AA; 27114 MW; 00459EF10710E925 CRC64;
MGRAPAKRKP SSPPPPPPPG RCHFWLPNKR RHCANTPLPT SQYCGNHLPD SASDAGAPFR
RLVPCPVDPS HTVLEENLEA HVGKCPLKKQ AAALAAQPFY SKGINSGGGE GGGGVTSAAK
RALVHKLTKD ELRALIEKIK LAHASAAMAM RDSFLVTDAC DNWMRNQVDR KVPYQEKHVT
QQASIIGNME AFGLLQKGGE VAEENGVKNA PAVVEFGAGR GYLTQMLADC YGIRNVFLVE
RRSYKLKLKI
