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Database: UniProt
Entry: U2EJV7_9GAMM
LinkDB: U2EJV7_9GAMM
Original site: U2EJV7_9GAMM 
ID   U2EJV7_9GAMM            Unreviewed;       447 AA.
AC   U2EJV7;
DT   13-NOV-2013, integrated into UniProtKB/TrEMBL.
DT   13-NOV-2013, sequence version 1.
DT   24-JAN-2024, entry version 49.
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   ECO:0000313|EMBL:ERJ18290.1};
GN   ORFNames=SSPSH_002918 {ECO:0000313|EMBL:ERJ18290.1};
OS   Salinisphaera shabanensis E1L3A.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Salinisphaerales;
OC   Salinisphaeraceae; Salinisphaera.
OX   NCBI_TaxID=1033802 {ECO:0000313|EMBL:ERJ18290.1, ECO:0000313|Proteomes:UP000006242};
RN   [1] {ECO:0000313|EMBL:ERJ18290.1, ECO:0000313|Proteomes:UP000006242}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=E1L3A {ECO:0000313|EMBL:ERJ18290.1,
RC   ECO:0000313|Proteomes:UP000006242};
RX   PubMed=21705588; DOI=10.1128/JB.05459-11;
RA   Antunes A., Alam I., Bajic V.B., Stingl U.;
RT   "Genome sequence of Salinisphaera shabanensis, a gammaproteobacterium from
RT   the harsh, variable environment of the brine-seawater interface of the
RT   Shaban Deep in the Red Sea.";
RL   J. Bacteriol. 193:4555-4556(2011).
RN   [2] {ECO:0000313|EMBL:ERJ18290.1, ECO:0000313|Proteomes:UP000006242}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=E1L3A {ECO:0000313|EMBL:ERJ18290.1,
RC   ECO:0000313|Proteomes:UP000006242};
RX   PubMed=24324765;
RA   Alam I., Antunes A., Kamau A.A., Ba Alawi W., Kalkatawi M., Stingl U.,
RA   Bajic V.B.;
RT   "INDIGO - INtegrated Data Warehouse of MIcrobial GenOmes with Examples from
RT   the Red Sea Extremophiles.";
RL   PLoS ONE 8:E82210-E82210(2013).
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:ERJ18290.1}.
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DR   EMBL; AFNV02000021; ERJ18290.1; -; Genomic_DNA.
DR   RefSeq; WP_006915387.1; NZ_AFNV02000021.1.
DR   AlphaFoldDB; U2EJV7; -.
DR   STRING; 1033802.SSPSH_002918; -.
DR   eggNOG; COG2265; Bacteria.
DR   OrthoDB; 9804590at2; -.
DR   Proteomes; UP000006242; 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; 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; 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; 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}; Reference proteome {ECO:0000313|Proteomes:UP000006242};
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   ACT_SITE        398
FT                   /evidence="ECO:0000256|PROSITE-ProRule:PRU10015"
FT   ACT_SITE        398
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010,
FT                   ECO:0000256|PROSITE-ProRule:PRU01024"
FT   BINDING         78
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         84
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         87
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         166
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         274
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         303
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   BINDING         324
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         351
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01010"
FT   BINDING         372
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   447 AA;  49430 MW;  6977E8C4167DAB33 CRC64;
     MSRRQRRRKP ADRGIVDIVD LASNARGVGH VDGKAVFVAD TLPGEQALYR PTKQKKSYEE
     ASLETLFSAS DKRVTPRCAH FGLCGGCALQ HAGENAQLEF KQGQLLAALE RVGKVEPDTV
     LAPLVDTRWG YRRRARLGVK YVEKKGGTLV GFRERGAPFI ALLDRCEVLV APVGNRLTDL
     AELIDGLSIR ERLPQIEVAA ADNVIALVFR VLDDPTEADR ERLREFGARF EFSIYLQPGN
     EDTIAPLDAE APALYYELPD WDARLYFKPN DFVQIHAGIN ARMIAQALDL LEVDDSHQVL
     ELFSGLGNFS IPLARQAARV ITVEGEEGLV ERAQENARFN GLDNIEAHVA NLFEPPEEAA
     WRREKVDRVL IDPPRSGAAE MLESIAATGA ERIVYCSCHP ATLARDAGEL VHRYGYRLTH
     AGVMDMFPHT AHVESMAVFV KQGGEGA
//
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