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Dual-specificity RNA methyltransferase RlmN (EC 2.1.1.192) (23S rRNA (adenine(2503)-C(2))-methyltransferase) (23S rRNA m2A2503 methyltransferase) (Ribosomal RNA large subunit methyltransferase N) (tRNA (adenine(37)-C(2))-methyltransferase) (tRNA m2A37 methyltransferase)

 A0A1B4X444_9PSED        Unreviewed;       381 AA.
A0A1B4X444;
02-NOV-2016, integrated into UniProtKB/TrEMBL.
02-NOV-2016, sequence version 1.
16-JAN-2019, entry version 15.
RecName: Full=Dual-specificity RNA methyltransferase RlmN {ECO:0000256|HAMAP-Rule:MF_01849};
EC=2.1.1.192 {ECO:0000256|HAMAP-Rule:MF_01849};
AltName: Full=23S rRNA (adenine(2503)-C(2))-methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849};
AltName: Full=23S rRNA m2A2503 methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849};
AltName: Full=Ribosomal RNA large subunit methyltransferase N {ECO:0000256|HAMAP-Rule:MF_01849};
AltName: Full=tRNA (adenine(37)-C(2))-methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849};
AltName: Full=tRNA m2A37 methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849};
Name=rlmN {ECO:0000256|HAMAP-Rule:MF_01849};
ORFNames=LAB08_4290 {ECO:0000313|EMBL:BAV29560.1};
Pseudomonas sp. LAB-08.
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
Pseudomonadaceae; Pseudomonas.
NCBI_TaxID=143813 {ECO:0000313|EMBL:BAV29560.1, ECO:0000313|Proteomes:UP000218595};
[1] {ECO:0000313|EMBL:BAV29560.1, ECO:0000313|Proteomes:UP000218595}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Suzuki K., Fatma A., Inuzuka Y., Tashiro Y., Futamata H.;
"Draft genome sequence of Pseudomonassp. LAB-08 isolated from TCE
contaminated aquifer soil.";
Submitted (APR-2016) to the EMBL/GenBank/DDBJ databases.
-!- FUNCTION: Specifically methylates position 2 of adenine 2503 in
23S rRNA and position 2 of adenine 37 in tRNAs. m2A2503
modification seems to play a crucial role in the proofreading step
occurring at the peptidyl transferase center and thus would serve
to optimize ribosomal fidelity. {ECO:0000256|HAMAP-Rule:MF_01849}.
-!- CATALYTIC ACTIVITY:
Reaction=adenosine(2503) in 23S rRNA + 2 reduced [2Fe-2S]-
[ferredoxin] + 2 S-adenosyl-L-methionine = 2-
methyladenosine(2503) in 23S rRNA + 5'-deoxyadenosine + L-
methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-
homocysteine; Xref=Rhea:RHEA:42916, Rhea:RHEA-COMP:10000,
Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10152, Rhea:RHEA-
COMP:10282, ChEBI:CHEBI:17319, ChEBI:CHEBI:33737,
ChEBI:CHEBI:33738, ChEBI:CHEBI:57844, ChEBI:CHEBI:57856,
ChEBI:CHEBI:59789, ChEBI:CHEBI:74411, ChEBI:CHEBI:74497;
EC=2.1.1.192; Evidence={ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS01114928};
-!- CATALYTIC ACTIVITY:
Reaction=adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] +
2 S-adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'-
deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin]
+ S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:43332, Rhea:RHEA-
COMP:10000, Rhea:RHEA-COMP:10001, Rhea:RHEA-COMP:10162,
Rhea:RHEA-COMP:10485, ChEBI:CHEBI:17319, ChEBI:CHEBI:33737,
ChEBI:CHEBI:33738, ChEBI:CHEBI:57844, ChEBI:CHEBI:57856,
ChEBI:CHEBI:59789, ChEBI:CHEBI:74411, ChEBI:CHEBI:74497;
EC=2.1.1.192; Evidence={ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS01114934};
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000256|HAMAP-Rule:MF_01849};
Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
cysteines and an exchangeable S-adenosyl-L-methionine.
{ECO:0000256|HAMAP-Rule:MF_01849};
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00385725}.
-!- MISCELLANEOUS: Reaction proceeds by a ping-pong mechanism
involving intermediate methylation of a conserved cysteine
residue. {ECO:0000256|HAMAP-Rule:MF_01849}.
-!- SIMILARITY: Belongs to the radical SAM superfamily. RlmN family.
{ECO:0000256|HAMAP-Rule:MF_01849, ECO:0000256|SAAS:SAAS00571858}.
-!- CAUTION: Lacks conserved residue(s) required for the propagation
of feature annotation. {ECO:0000256|HAMAP-Rule:MF_01849}.
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EMBL; AP017423; BAV29560.1; -; Genomic_DNA.
Proteomes; UP000218595; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0070040; F:rRNA (adenine-C2-)-methyltransferase activity; IEA:UniProtKB-UniRule.
GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-UniRule.
GO; GO:0002935; F:tRNA (adenine-C2-)-methyltransferase activity; IEA:UniProtKB-UniRule.
GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-UniRule.
GO; GO:0070475; P:rRNA base methylation; IEA:UniProtKB-UniRule.
Gene3D; 3.20.20.70; -; 1.
HAMAP; MF_01849; RNA_methyltr_RlmN; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR040072; Methyltransferase_A.
InterPro; IPR027492; RNA_MTrfase_RlmN.
InterPro; IPR004383; rRNA_lsu_MTrfase_RlmN/Cfr.
InterPro; IPR007197; rSAM.
PANTHER; PTHR30544; PTHR30544; 1.
Pfam; PF04055; Radical_SAM; 1.
PIRSF; PIRSF006004; CHP00048; 1.
SFLD; SFLDF00275; adenosine_C2_methyltransferase; 1.
TIGRFAMs; TIGR00048; rRNA_mod_RlmN; 1.
3: Inferred from homology;
4Fe-4S {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00463035};
Complete proteome {ECO:0000313|Proteomes:UP000218595};
Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00462865};
Disulfide bond {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00721829};
Iron {ECO:0000256|HAMAP-Rule:MF_01849, ECO:0000256|SAAS:SAAS00463035};
Iron-sulfur {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00463035};
Metal-binding {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00463035};
Methyltransferase {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00462825, ECO:0000313|EMBL:BAV29560.1};
rRNA processing {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00536180};
S-adenosyl-L-methionine {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00462941};
Transferase {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00462825, ECO:0000313|EMBL:BAV29560.1};
tRNA processing {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00721837}.
DOMAIN 111 285 Radical_SAM. {ECO:0000259|Pfam:PF04055}.
REGION 170 171 S-adenosyl-L-methionine binding.
{ECO:0000256|HAMAP-Rule:MF_01849}.
REGION 224 226 S-adenosyl-L-methionine binding.
{ECO:0000256|HAMAP-Rule:MF_01849}.
ACT_SITE 96 96 Proton acceptor. {ECO:0000256|HAMAP-
Rule:MF_01849}.
ACT_SITE 345 345 S-methylcysteine intermediate.
{ECO:0000256|HAMAP-Rule:MF_01849}.
METAL 116 116 Iron-sulfur (4Fe-4S-S-AdoMet).
{ECO:0000256|HAMAP-Rule:MF_01849}.
METAL 120 120 Iron-sulfur (4Fe-4S-S-AdoMet).
{ECO:0000256|HAMAP-Rule:MF_01849}.
METAL 123 123 Iron-sulfur (4Fe-4S-S-AdoMet).
{ECO:0000256|HAMAP-Rule:MF_01849}.
BINDING 202 202 S-adenosyl-L-methionine.
{ECO:0000256|HAMAP-Rule:MF_01849}.
BINDING 302 302 S-adenosyl-L-methionine; via amide
nitrogen and carbonyl oxygen.
{ECO:0000256|HAMAP-Rule:MF_01849}.
SEQUENCE 381 AA; 42163 MW; 3852D56D2BEC9A0D CRC64;
MTTSTVKTNL LGLTQPEMEK FFDSIGEKRF RAGQVMKWIH HFGVDDFDAM TNVSKALREK
LKAVAEVRGP EVVSEDISSD GTRKWVVRVA SGSCVETVYI PQGKRGTLCV SSQAGCALDC
SFCSTGKQGF NSNLTAAEVI GQVWIANKSF GSVPATVDRA ITNVVMMGMG EPLLNFDNVI
AAMHLMMDDL GYGISKRRVT LSTSGVVPMI DELSKHIDVS LALSLHAPND ALRNQLVPIN
KKYPLKMLLE SCQRYMSSLG EKRVLTIEYT LLKDVNDKVE HAVEMIELLK NIPCKINLIP
FNPFPHSGYE RPSNNAIRRF QDQLHHAGFN VTVRTTRGED IDAACGQLVG QVLDRTRRSE
RYIAVRELNA DSDLAQNAAN K


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