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Database: UniProt
Entry: C0QKU6_DESAH
LinkDB: C0QKU6_DESAH
Original site: C0QKU6_DESAH 
ID   C0QKU6_DESAH            Unreviewed;       345 AA.
AC   C0QKU6;
DT   05-MAY-2009, integrated into UniProtKB/TrEMBL.
DT   05-MAY-2009, sequence version 1.
DT   24-JAN-2024, entry version 86.
DE   RecName: Full=Probable 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   OrderedLocusNames=HRM2_31030 {ECO:0000313|EMBL:ACN16186.1};
OS   Desulforapulum autotrophicum (strain ATCC 43914 / DSM 3382 / VKM B-1955 /
OS   HRM2) (Desulfobacterium autotrophicum).
OC   Bacteria; Thermodesulfobacteriota; Desulfobacteria; Desulfobacterales;
OC   Desulfobacteraceae; Desulforapulum.
OX   NCBI_TaxID=177437 {ECO:0000313|EMBL:ACN16186.1, ECO:0000313|Proteomes:UP000000442};
RN   [1] {ECO:0000313|EMBL:ACN16186.1, ECO:0000313|Proteomes:UP000000442}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 43914 / DSM 3382 / HRM2
RC   {ECO:0000313|Proteomes:UP000000442};
RX   PubMed=19187283; DOI=10.1111/j.1462-2920.2008.01825.x;
RA   Strittmatter A.W., Liesegang H., Rabus R., Decker I., Amann J., Andres S.,
RA   Henne A., Fricke W.F., Martinez-Arias R., Bartels D., Goesmann A.,
RA   Krause L., Puehler A., Klenk H.P., Richter M., Schuler M., Gloeckner F.O.,
RA   Meyerdierks A., Gottschalk G., Amann R.;
RT   "Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate
RT   reducer oxidizing organic carbon completely to carbon dioxide.";
RL   Environ. Microbiol. 11:1038-1055(2009).
CC   -!- FUNCTION: Specifically methylates position 2 of adenine 2503 in 23S
CC       rRNA and position 2 of adenine 37 in tRNAs. {ECO:0000256|HAMAP-
CC       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|HAMAP-Rule:MF_01849}.
CC   -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC       feature annotation. {ECO:0000256|HAMAP-Rule:MF_01849}.
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DR   EMBL; CP001087; ACN16186.1; -; Genomic_DNA.
DR   AlphaFoldDB; C0QKU6; -.
DR   STRING; 177437.HRM2_31030; -.
DR   KEGG; dat:HRM2_31030; -.
DR   eggNOG; COG0820; Bacteria.
DR   HOGENOM; CLU_029101_0_0_7; -.
DR   OMA; QVGCSLD; -.
DR   OrthoDB; 9793973at2; -.
DR   Proteomes; UP000000442; Chromosome.
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 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; SFLDG01062; methyltransferase_(Class_A); 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|HAMAP-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:UP000000442};
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          96..331
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000259|PROSITE:PS51918"
FT   ACT_SITE        90
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT   ACT_SITE        336
FT                   /note="S-methylcysteine intermediate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT   BINDING         110
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         114
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         117
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         162..163
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT   BINDING         195
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT   BINDING         217..219
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
FT   BINDING         293
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01849"
SQ   SEQUENCE   345 AA;  39275 MW;  34E822DD68DCE768 CRC64;
     MKEITDFTRQ ELTAWFENNN ERSFRGGQVF KWLYLRQAQT FDEMTDIGKD LRQRLKENFT
     LSAMVFDRSE ISRDGTEKLL FRLHDNAYIE AVLIPEKDHF TLCISSQAGC AQGCKFCLTA
     KGGFTRNLTT GEIIGQIRTA KTVLAKRKAQ RPLSNIVFMG MGEPLANYDT VVRALSIMTD
     SDYGLKLSSR RITLSTCGLV PEILRLGNDT EVNLAVSLNA TTDETRSMLM PINRRYPMHE
     LLKACTNFQM KPRKKITFEY ILIKNVNDTM DDAKRLITLL LPIRAKVNLI PFNEHDQSDF
     KRPSKESILA FLQMLLDHNL TAMVRKSKGD DISAACGQLR AKADL
//
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