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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)

 A0A1W9NMT4_9GAMM        Unreviewed;       361 AA.
A0A1W9NMT4;
05-JUL-2017, integrated into UniProtKB/TrEMBL.
05-JUL-2017, sequence version 1.
16-JAN-2019, entry version 7.
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=B0D82_00195 {ECO:0000313|EMBL:OQX42952.1};
Gammaproteobacteria bacterium LUC003_P10.
Bacteria; Proteobacteria; Gammaproteobacteria;
sulfur-oxidizing symbionts.
NCBI_TaxID=1940812 {ECO:0000313|EMBL:OQX42952.1};
[1] {ECO:0000313|EMBL:OQX42952.1}
NUCLEOTIDE SEQUENCE.
STRAIN=LUC003_P10 {ECO:0000313|EMBL:OQX42952.1};
Lim S.J., Davis B.G., Gill D.E., Engel A.S., Anderson L.C.,
Campbell B.J.;
"Novel co-symbiosis in the unique lucinid bivalve Phacoides
pectinatus.";
Submitted (FEB-2017) 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}.
-!- CAUTION: The sequence shown here is derived from an
EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is
preliminary data. {ECO:0000313|EMBL:OQX42952.1}.
-----------------------------------------------------------------------
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EMBL; MUII01000012; OQX42952.1; -; Genomic_DNA.
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.
SFLD; SFLDS00029; Radical_SAM; 1.
TIGRFAMs; TIGR00048; rRNA_mod_RlmN; 1.
3: Inferred from homology;
4Fe-4S {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00463035};
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:OQX42952.1};
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:OQX42952.1};
tRNA processing {ECO:0000256|HAMAP-Rule:MF_01849,
ECO:0000256|SAAS:SAAS00721837}.
DOMAIN 110 276 Radical_SAM. {ECO:0000259|Pfam:PF04055}.
REGION 162 163 S-adenosyl-L-methionine binding.
{ECO:0000256|HAMAP-Rule:MF_01849}.
REGION 216 218 S-adenosyl-L-methionine binding.
{ECO:0000256|HAMAP-Rule:MF_01849}.
ACT_SITE 95 95 Proton acceptor. {ECO:0000256|HAMAP-
Rule:MF_01849}.
ACT_SITE 336 336 S-methylcysteine intermediate.
{ECO:0000256|HAMAP-Rule:MF_01849}.
METAL 115 115 Iron-sulfur (4Fe-4S-S-AdoMet).
{ECO:0000256|HAMAP-Rule:MF_01849}.
METAL 119 119 Iron-sulfur (4Fe-4S-S-AdoMet).
{ECO:0000256|HAMAP-Rule:MF_01849}.
METAL 122 122 Iron-sulfur (4Fe-4S-S-AdoMet).
{ECO:0000256|HAMAP-Rule:MF_01849}.
BINDING 194 194 S-adenosyl-L-methionine.
{ECO:0000256|HAMAP-Rule:MF_01849}.
BINDING 293 293 S-adenosyl-L-methionine; via amide
nitrogen and carbonyl oxygen.
{ECO:0000256|HAMAP-Rule:MF_01849}.
SEQUENCE 361 AA; 40511 MW; 1F2CAB8503024FF9 CRC64;
MVSDQKINLL GLERGAMEAL FVELGSKAFH GRNVLKWIHK HGVSDFSLMT DLPKRLRARL
EELAEVRVPE VVFDQPASDG THKWVLELEC GNRIESVYIP DGDRSTLCVS SQVGCSLDCS
FCSTARQGFN RNLSAAEIIG QVWVAARGMN KPLTNVVLMG MGEPLANFDA VVSAMEIMQD
DLTYMLSKYR VTVSTSGIVP AIYRLNEVSD VSLAVSLHAP NNALRDQLVP INRKYPLEEL
IPACREYVRG DKRRKVTWEY VMLDGVNDSI RHARELIRLL EGTPSKMNLI PFNPFPGTDY
RCSPPERIEA FRQKLMKAGI ISITRKTRGE DIDAACGQLV GKVRDRSRRE LRLARAVPRG
R


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