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Database: UniProt
Entry: D0RN88_9PROT
LinkDB: D0RN88_9PROT
Original site: D0RN88_9PROT 
ID   D0RN88_9PROT            Unreviewed;       357 AA.
AC   D0RN88;
DT   15-DEC-2009, integrated into UniProtKB/TrEMBL.
DT   15-DEC-2009, sequence version 1.
DT   24-JAN-2024, entry version 72.
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   ORFNames=HIMB114_00002530 {ECO:0000313|EMBL:EMH79882.1};
OS   alpha proteobacterium HIMB114.
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Candidatus Pelagibacterales;
OC   Candidatus Pelagibacteraceae.
OX   NCBI_TaxID=684719 {ECO:0000313|EMBL:EMH79882.1, ECO:0000313|Proteomes:UP000033990};
RN   [1] {ECO:0000313|EMBL:EMH79882.1, ECO:0000313|Proteomes:UP000033990}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=HIMB114 {ECO:0000313|EMBL:EMH79882.1,
RC   ECO:0000313|Proteomes:UP000033990};
RA   Rappe M., Ferriera S., Johnson J., Kravitz S., Beeson K., Sutton G.,
RA   Rogers Y.-H., Friedman R., Frazier M., Venter J.C.;
RL   Submitted (OCT-2009) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0000313|EMBL:EMH79882.1, ECO:0000313|Proteomes:UP000033990}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=HIMB114 {ECO:0000313|EMBL:EMH79882.1,
RC   ECO:0000313|Proteomes:UP000033990};
RA   Grote J., Thrash C., Huggett M.J., Landry Z., Carini P., Giovannoni S.J.,
RA   Rappe M.S., Brinkac L., Kim M., Beeson K., Ferriera S., Sutton G.,
RA   Friedman R., Venter J.C.;
RL   Submitted (SEP-2012) 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: Lacks conserved residue(s) required for the propagation of
CC       feature annotation. {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:EMH79882.1}.
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DR   EMBL; ADAC02000001; EMH79882.1; -; Genomic_DNA.
DR   AlphaFoldDB; D0RN88; -.
DR   STRING; 684719.HIMB114_00002530; -.
DR   eggNOG; COG0820; Bacteria.
DR   OrthoDB; 9793973at2; -.
DR   Proteomes; UP000033990; 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; 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 DOMAIN-CONTAINING PROTEIN; 1.
DR   Pfam; PF04055; Radical_SAM; 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:UP000033990};
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}; tRNA processing {ECO:0000256|HAMAP-Rule:MF_01849}.
FT   DOMAIN          101..335
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000259|PROSITE:PS51918"
FT   ACT_SITE        95
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT   ACT_SITE        340
FT                   /note="S-methylcysteine intermediate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT   BINDING         115
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         119
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         122
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         167..168
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT   BINDING         199
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT   BINDING         221..223
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT   BINDING         297
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
SQ   SEQUENCE   357 AA;  40944 MW;  6A2781D68A7D6738 CRC64;
     MIEFADLNYR EVKSIFSNNF NLDKKKSSMR ANQVWKFYYQ KGYSDPNLFS NLTQSLRDEL
     LKIVNFSRPK IKNKQVSKDG TIKWLLELND KNLVETVYIP SETHSTLCIS SQVGCTLNCK
     FCHTGIQPLV KNLSSNEIIS QILIAKDELN DWKEQKKINN IVYMGMGEPF YNFENIKKSV
     EILKDENGLN FSNKKITVST SGISPNIKKA ANEIGTYLAL SLHAPNNEIR NEIMPINKKY
     NIENIIEHCS QYAKENGEKI FIEYVLLKDV NDTEQCAKEL SKIMSQFPCK LNLIQFNPWP
     GVKYKTATKE QTSKFIEIIK KNGHVVTLRK SRGDDILGAC GQLKTASERE KRSTLSK
//
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