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Database: UniProt
Entry: A0A095UVT2_9GAMM
LinkDB: A0A095UVT2_9GAMM
Original site: A0A095UVT2_9GAMM 
ID   A0A095UVT2_9GAMM        Unreviewed;       446 AA.
AC   A0A095UVT2;
DT   26-NOV-2014, integrated into UniProtKB/TrEMBL.
DT   26-NOV-2014, sequence version 1.
DT   24-JAN-2024, entry version 44.
DE   RecName: Full=23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD {ECO:0000256|HAMAP-Rule:MF_01010};
DE            EC=2.1.1.190 {ECO:0000256|HAMAP-Rule:MF_01010};
DE   AltName: Full=23S rRNA(m5U1939)-methyltransferase {ECO:0000256|HAMAP-Rule:MF_01010};
GN   Name=rlmD {ECO:0000256|HAMAP-Rule:MF_01010};
GN   ORFNames=Y5S_00312 {ECO:0000313|EMBL:KGD66645.1};
OS   Alcanivorax nanhaiticus.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Oceanospirillales;
OC   Alcanivoracaceae; Alcanivorax.
OX   NCBI_TaxID=1177154 {ECO:0000313|EMBL:KGD66645.1, ECO:0000313|Proteomes:UP000029444};
RN   [1] {ECO:0000313|EMBL:KGD66645.1, ECO:0000313|Proteomes:UP000029444}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=19-m-6 {ECO:0000313|EMBL:KGD66645.1,
RC   ECO:0000313|Proteomes:UP000029444};
RA   Lai Q., Shao Z.;
RT   "Genome Sequence of alkane-degrading Bacterium Alcanivorax sp. 19-m-6.";
RL   Submitted (SEP-2012) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 1939
CC       (m5U1939) in 23S rRNA. {ECO:0000256|HAMAP-Rule:MF_01010}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=S-adenosyl-L-methionine + uridine(1939) in 23S rRNA = 5-
CC         methyluridine(1939) in 23S rRNA + H(+) + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:42908, Rhea:RHEA-COMP:10278, Rhea:RHEA-COMP:10279,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC         ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; EC=2.1.1.190;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01010};
CC   -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC       superfamily. RNA M5U methyltransferase family. RlmD subfamily.
CC       {ECO:0000256|HAMAP-Rule:MF_01010}.
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:KGD66645.1}.
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DR   EMBL; ARXV01000001; KGD66645.1; -; Genomic_DNA.
DR   RefSeq; WP_035229715.1; NZ_ARXV01000001.1.
DR   AlphaFoldDB; A0A095UVT2; -.
DR   STRING; 1177154.Y5S_00312; -.
DR   PATRIC; fig|1177154.3.peg.315; -.
DR   eggNOG; COG2265; Bacteria.
DR   OrthoDB; 9804590at2; -.
DR   Proteomes; UP000029444; Unassembled WGS sequence.
DR   GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR   GO; GO:0005506; F:iron ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0070041; F:rRNA (uridine-C5-)-methyltransferase activity; IEA:UniProtKB-UniRule.
DR   CDD; cd02440; AdoMet_MTases; 1.
DR   Gene3D; 2.40.50.1070; -; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR   Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 1.
DR   HAMAP; MF_01010; 23SrRNA_methyltr_RlmD; 1.
DR   InterPro; IPR001566; 23S_rRNA_MeTrfase_RlmD.
DR   InterPro; IPR030390; MeTrfase_TrmA_AS.
DR   InterPro; IPR030391; MeTrfase_TrmA_CS.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   InterPro; IPR029063; SAM-dependent_MTases_sf.
DR   InterPro; IPR002792; TRAM_dom.
DR   InterPro; IPR010280; U5_MeTrfase_fam.
DR   NCBIfam; TIGR00479; rumA; 1.
DR   PANTHER; PTHR11061; RNA M5U METHYLTRANSFERASE; 1.
DR   PANTHER; PTHR11061:SF30; TRNA (URACIL(54)-C(5))-METHYLTRANSFERASE; 1.
DR   Pfam; PF01938; TRAM; 1.
DR   Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 1.
DR   PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
DR   PROSITE; PS50926; TRAM; 1.
DR   PROSITE; PS01230; TRMA_1; 1.
DR   PROSITE; PS01231; TRMA_2; 1.
PE   3: Inferred from homology;
KW   4Fe-4S {ECO:0000256|HAMAP-Rule:MF_01010};
KW   Iron {ECO:0000256|HAMAP-Rule:MF_01010};
KW   Iron-sulfur {ECO:0000256|HAMAP-Rule:MF_01010};
KW   Metal-binding {ECO:0000256|HAMAP-Rule:MF_01010};
KW   Methyltransferase {ECO:0000256|ARBA:ARBA00022603, ECO:0000256|HAMAP-
KW   Rule:MF_01010};
KW   rRNA processing {ECO:0000256|ARBA:ARBA00022552, ECO:0000256|HAMAP-
KW   Rule:MF_01010};
KW   S-adenosyl-L-methionine {ECO:0000256|ARBA:ARBA00022691, ECO:0000256|HAMAP-
KW   Rule:MF_01010};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW   Rule:MF_01010}.
FT   DOMAIN          5..64
FT                   /note="TRAM"
FT                   /evidence="ECO:0000259|PROSITE:PS50926"
FT   REGION          1..31
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        403
FT                   /evidence="ECO:0000256|PROSITE-ProRule:PRU10015"
FT   ACT_SITE        403
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT                   ECO:0000256|PROSITE-ProRule:PRU01024"
FT   BINDING         77
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         83
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         86
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         165
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         279
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT                   ECO:0000256|PROSITE-ProRule:PRU01024"
FT   BINDING         308
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT                   ECO:0000256|PROSITE-ProRule:PRU01024"
FT   BINDING         313
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         329
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT                   ECO:0000256|PROSITE-ProRule:PRU01024"
FT   BINDING         356
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         377
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT                   ECO:0000256|PROSITE-ProRule:PRU01024"
SQ   SEQUENCE   446 AA;  49765 MW;  2502410C2E1B06E8 CRC64;
     MARKRKPLPE TPEPASIESL SHDGRGIARR DGKTTFIDNA LPGEEVMFKF TYMRKKFDEG
     KAVEIIKASP DRVTPPCQHS TLCGGCSLQH MSPDVQIARK EAVLREQLQH FGGLEPKEWL
     PPLTGPVTGY RSKARMGVKY VEAKDETLVG FREKRNSFIA QLHGCEVLVP EVGHRLDDLR
     ALMHGLKSRT RIPQIELAAG DDIVALIIRH LDPLPDEDQQ ALLNFCQPLG WHLYLQPGNE
     STVHRIWPAL TGAEHEERLY YRHPSADVEL AFHPTDFTQV NADINRKMVP LALDLLDIAP
     EHTVLDLFCG LGNFTIPAAK RAAKVVGVEV SQAMVKRGYE NAARNGLNNL DFHAWDLSQD
     IAGQVWASKA YDRILIDPPR TGALEMVKLM PRFGAKKIVY VSCNPATLAR DAGELTALGY
     RLKAAGVMDM FPHTTHVESI ALFEKK
//
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