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RLMN_ALIB4
ID   RLMN_ALIB4              Reviewed;         360 AA.
AC   A8EQW8;
DT   02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT   13-NOV-2007, sequence version 1.
DT   03-AUG-2022, entry version 80.
DE   RecName: Full=Dual-specificity RNA methyltransferase RlmN {ECO:0000255|HAMAP-Rule:MF_01849};
DE            EC=2.1.1.192 {ECO:0000255|HAMAP-Rule:MF_01849};
DE   AltName: Full=23S rRNA (adenine(2503)-C(2))-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01849};
DE   AltName: Full=23S rRNA m2A2503 methyltransferase {ECO:0000255|HAMAP-Rule:MF_01849};
DE   AltName: Full=Ribosomal RNA large subunit methyltransferase N {ECO:0000255|HAMAP-Rule:MF_01849};
DE   AltName: Full=tRNA (adenine(37)-C(2))-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01849};
DE   AltName: Full=tRNA m2A37 methyltransferase {ECO:0000255|HAMAP-Rule:MF_01849};
GN   Name=rlmN {ECO:0000255|HAMAP-Rule:MF_01849}; OrderedLocusNames=Abu_0057;
OS   Aliarcobacter butzleri (strain RM4018) (Arcobacter butzleri).
OC   Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC   Arcobacteraceae; Aliarcobacter.
OX   NCBI_TaxID=367737;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=RM4018;
RX   PubMed=18159241; DOI=10.1371/journal.pone.0001358;
RA   Miller W.G., Parker C.T., Rubenfield M., Mendz G.L., Woesten M.M.S.M.,
RA   Ussery D.W., Stolz J.F., Binnewies T.T., Hallin P.F., Wang G., Malek J.A.,
RA   Rogosin A., Stanker L.H., Mandrell R.E.;
RT   "The complete genome sequence and analysis of the Epsilonproteobacterium
RT   Arcobacter butzleri.";
RL   PLoS ONE 2:E1358-E1358(2007).
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:0000255|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:0000255|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:0000255|HAMAP-Rule:MF_01849};
CC   -!- COFACTOR:
CC       Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC         Evidence={ECO:0000255|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:0000255|HAMAP-Rule:MF_01849};
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01849}.
CC   -!- MISCELLANEOUS: Reaction proceeds by a ping-pong mechanism involving
CC       intermediate methylation of a conserved cysteine residue.
CC       {ECO:0000255|HAMAP-Rule:MF_01849}.
CC   -!- SIMILARITY: Belongs to the radical SAM superfamily. RlmN family.
CC       {ECO:0000255|HAMAP-Rule:MF_01849}.
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DR   EMBL; CP000361; ABV66342.1; -; Genomic_DNA.
DR   RefSeq; WP_012011967.1; NC_009850.1.
DR   AlphaFoldDB; A8EQW8; -.
DR   SMR; A8EQW8; -.
DR   STRING; 367737.Abu_0057; -.
DR   EnsemblBacteria; ABV66342; ABV66342; Abu_0057.
DR   KEGG; abu:Abu_0057; -.
DR   eggNOG; COG0820; Bacteria.
DR   HOGENOM; CLU_029101_2_0_7; -.
DR   OMA; QVGCSLD; -.
DR   OrthoDB; 1111428at2; -.
DR   Proteomes; UP000001136; 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-C2-)-methyltransferase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0002935; F:tRNA (adenine-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   Gene3D; 3.20.20.70; -; 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   PANTHER; PTHR30544; PTHR30544; 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   TIGRFAMs; TIGR00048; rRNA_mod_RlmN; 1.
DR   PROSITE; PS51918; RADICAL_SAM; 1.
PE   3: Inferred from homology;
KW   4Fe-4S; Cytoplasm; Disulfide bond; Iron; Iron-sulfur; Metal-binding;
KW   Methyltransferase; Reference proteome; rRNA processing;
KW   S-adenosyl-L-methionine; Transferase; tRNA processing.
FT   CHAIN           1..360
FT                   /note="Dual-specificity RNA methyltransferase RlmN"
FT                   /id="PRO_0000350019"
FT   DOMAIN          110..343
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT   ACT_SITE        91
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   ACT_SITE        348
FT                   /note="S-methylcysteine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   BINDING         124
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   BINDING         128
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   BINDING         131
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_note="4Fe-4S-S-AdoMet"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   BINDING         174..175
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   BINDING         206
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   BINDING         229..231
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   BINDING         305
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
FT   DISULFID        117..348
FT                   /note="(transient)"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01849"
SQ   SEQUENCE   360 AA;  40818 MW;  6C27FB211CE0B48C CRC64;
     MAKEALPSIY DYTLDELKEI LKPSFRAKQV YNWLYKKYAS SYDEMKNLPK ELVEDLKENY
     PIDIMQIVKK EQSRDGSIKY LFKLRDNHTV EAVLLLMKDK KIDEDGQIVR SEKYTVCISS
     QVGCKVGCSF CLTAKGGFVR NLTVGEYIAQ IVNIKRDNDI AENKALNIVY MGMGEPLDNF
     DNFTKAVEIF SELDGLAISR RRQTVSTSGI ATKIKKLGEK DLQIQLAISL HAVDDELRSE
     LIPMNKAYNI ASIIQAVKAF PVDTRKKVMF EYLVIKDKND SIEAAKKLVS LLNGIQAKVN
     LIYFNPYPGT SYQRPQEKDM LKFKDFLNQK GVICTIRESK GLDISAACGQ LKEKEANGNS
 
 
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