ID A0A085JHR8_9GAMM Unreviewed; 391 AA.
AC A0A085JHR8;
DT 29-OCT-2014, integrated into UniProtKB/TrEMBL.
DT 29-OCT-2014, sequence version 1.
DT 27-MAR-2024, entry version 42.
DE RecName: Full=Dual-specificity RNA methyltransferase RlmN {ECO:0000256|HAMAP-Rule:MF_01849};
DE EC=2.1.1.192 {ECO:0000256|HAMAP-Rule:MF_01849};
DE AltName: Full=23S rRNA (adenine(2503)-C(2))-methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849};
DE AltName: Full=23S rRNA m2A2503 methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849};
DE AltName: Full=Ribosomal RNA large subunit methyltransferase N {ECO:0000256|HAMAP-Rule:MF_01849};
DE AltName: Full=tRNA (adenine(37)-C(2))-methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849};
DE AltName: Full=tRNA m2A37 methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849};
GN Name=rlmN {ECO:0000256|HAMAP-Rule:MF_01849,
GN ECO:0000313|EMBL:KFD20014.1};
GN ORFNames=GTPT_1461 {ECO:0000313|EMBL:KFD20014.1};
OS Tatumella ptyseos ATCC 33301.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Erwiniaceae; Tatumella.
OX NCBI_TaxID=1005995 {ECO:0000313|EMBL:KFD20014.1, ECO:0000313|Proteomes:UP000028602};
RN [1] {ECO:0000313|EMBL:KFD20014.1, ECO:0000313|Proteomes:UP000028602}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33301 {ECO:0000313|EMBL:KFD20014.1,
RC ECO:0000313|Proteomes:UP000028602};
RA Plunkett G.III., Neeno-Eckwall E.C., Glasner J.D., Perna N.T.;
RT "ATOL: Assembling a taxonomically balanced genome-scale reconstruction of
RT the evolutionary history of the Enterobacteriaceae.";
RL Submitted (MAY-2014) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Specifically methylates position 2 of adenine 2503 in 23S
CC rRNA and position 2 of adenine 37 in tRNAs. m2A2503 modification seems
CC to play a crucial role in the proofreading step occurring at the
CC peptidyl transferase center and thus would serve to optimize ribosomal
CC fidelity. {ECO:0000256|HAMAP-Rule:MF_01849}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin]
CC + 2 S-adenosyl-L-methionine = 2-methyladenosine(2503) in 23S rRNA +
CC 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] +
CC S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:42916, Rhea:RHEA-
CC COMP:10000, Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10152, Rhea:RHEA-
CC COMP:10282, ChEBI:CHEBI:17319, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74497; EC=2.1.1.192;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01849};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-
CC adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-
CC deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-
CC adenosyl-L-homocysteine; Xref=Rhea:RHEA:43332, Rhea:RHEA-COMP:10000,
CC Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10162, Rhea:RHEA-COMP:10485,
CC ChEBI:CHEBI:17319, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738,
CC ChEBI:CHEBI:57844, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74497; EC=2.1.1.192;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01849};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01849};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000256|HAMAP-Rule:MF_01849};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01849}.
CC -!- MISCELLANEOUS: Reaction proceeds by a ping-pong mechanism involving
CC intermediate methylation of a conserved cysteine residue.
CC {ECO:0000256|HAMAP-Rule:MF_01849}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. RlmN family.
CC {ECO:0000256|ARBA:ARBA00007544, ECO:0000256|HAMAP-Rule:MF_01849}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KFD20014.1}.
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DR EMBL; JMPR01000027; KFD20014.1; -; Genomic_DNA.
DR RefSeq; WP_025903656.1; NZ_JMPR01000027.1.
DR AlphaFoldDB; A0A085JHR8; -.
DR eggNOG; COG0820; Bacteria.
DR OrthoDB; 9793973at2; -.
DR Proteomes; UP000028602; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0070040; F:rRNA (adenine(2503)-C2-)-methyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0002935; F:tRNA (adenine(37)-C2)-methyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0070475; P:rRNA base methylation; IEA:UniProtKB-UniRule.
DR GO; GO:0030488; P:tRNA methylation; IEA:UniProtKB-UniRule.
DR CDD; cd01335; Radical_SAM; 1.
DR Gene3D; 1.10.150.530; -; 1.
DR Gene3D; 3.20.20.70; Aldolase class I; 1.
DR HAMAP; MF_01849; RNA_methyltr_RlmN; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR040072; Methyltransferase_A.
DR InterPro; IPR048641; RlmN_N.
DR InterPro; IPR027492; RNA_MTrfase_RlmN.
DR InterPro; IPR004383; rRNA_lsu_MTrfase_RlmN/Cfr.
DR InterPro; IPR007197; rSAM.
DR NCBIfam; TIGR00048; rRNA_mod_RlmN; 1.
DR PANTHER; PTHR30544; 23S RRNA METHYLTRANSFERASE; 1.
DR PANTHER; PTHR30544:SF5; RADICAL SAM CORE DOMAIN-CONTAINING PROTEIN; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR Pfam; PF21016; RlmN_N; 1.
DR PIRSF; PIRSF006004; CHP00048; 1.
DR SFLD; SFLDF00275; adenosine_C2_methyltransferase; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SUPFAM; SSF102114; Radical SAM enzymes; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 3: Inferred from homology;
KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|HAMAP-Rule:MF_01849};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_01849};
KW Disulfide bond {ECO:0000256|ARBA:ARBA00023157, ECO:0000256|HAMAP-
KW Rule:MF_01849};
KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_01849};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP-
KW Rule:MF_01849};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01849};
KW Methyltransferase {ECO:0000256|ARBA:ARBA00022603, ECO:0000256|HAMAP-
KW Rule:MF_01849}; Reference proteome {ECO:0000313|Proteomes:UP000028602};
KW rRNA processing {ECO:0000256|ARBA:ARBA00022552, ECO:0000256|HAMAP-
KW Rule:MF_01849};
KW S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691, ECO:0000256|HAMAP-
KW Rule:MF_01849};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_01849};
KW tRNA processing {ECO:0000256|ARBA:ARBA00022694, ECO:0000256|HAMAP-
KW Rule:MF_01849}.
FT DOMAIN 116..355
FT /note="Radical SAM core"
FT /evidence="ECO:0000259|PROSITE:PS51918"
FT ACT_SITE 110
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT ACT_SITE 360
FT /note="S-methylcysteine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 130
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 134
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 137
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 184..185
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 216
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 238..240
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT BINDING 317
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT DISULFID 123..360
FT /note="(transient)"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
SQ SEQUENCE 391 AA; 43669 MW; B7546526469DF749 CRC64;
MSEPAATPVS DTPVTVTPKN TKINLLDLNR QQMREFFLEM GEKPFRADQV MKWMYHYCSD
DFEQMTDINK VLRQKLARVA EIRAPEVAEE MRSSDGTIKW AIRVGDQLVE TVYIPEDDRA
TLCVSSQVGC ALECKFCSTA QQGFNRNLRV SEIIGQVWRA AKIIGAAKVT GQRPITNVVM
MGMGEPLLNL TNVVPAMEIM LDDFGFGLSK RRVTLSTSGV VPALDKLGDM IDVALAISLH
APNDALRDDI VPINKKYNIE AFLQSVKRYM EKSNANQGRV TVEYVMLDHV NDSTDDAHQL
AEVLKDTPCK INLIPWNPFP GAPYGRSSNS RVDRFSKVLM EYGFTTIVRK TRGDDIDAAC
GQLAGDVIDR TKRTMRKKIA GEEISVKTVQ A
//
