RLMH_STAAU
ID RLMH_STAAU Reviewed; 159 AA.
AC P0C1V0; P0A0N8; Q9WVW7;
DT 05-SEP-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-SEP-2006, sequence version 1.
DT 03-AUG-2022, entry version 83.
DE RecName: Full=Ribosomal RNA large subunit methyltransferase H {ECO:0000255|HAMAP-Rule:MF_00658};
DE EC=2.1.1.177 {ECO:0000255|HAMAP-Rule:MF_00658};
DE AltName: Full=23S rRNA (pseudouridine1915-N3)-methyltransferase {ECO:0000255|HAMAP-Rule:MF_00658};
DE AltName: Full=23S rRNA m3Psi1915 methyltransferase {ECO:0000255|HAMAP-Rule:MF_00658};
DE AltName: Full=rRNA (pseudouridine-N3-)-methyltransferase RlmH {ECO:0000255|HAMAP-Rule:MF_00658};
GN Name=rlmH {ECO:0000255|HAMAP-Rule:MF_00658};
OS Staphylococcus aureus.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=1280;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=HUC19;
RX PubMed=10858352; DOI=10.1128/aac.44.7.1906-1910.2000;
RA Oliveira D.C., Wu S.W., de Lencastre H.;
RT "Genetic organization of the downstream region of the mecA element in
RT methicillin-resistant Staphylococcus aureus isolates carrying different
RT polymorphisms of this region.";
RL Antimicrob. Agents Chemother. 44:1906-1910(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=85/2082, 85/3907,
RC ATCC 25923 / DSM 1104 / JCM 2413 / NBRC 14462 / NCIMB 12702 / NCTC 12981 /
RC Seattle 1945, and NCTC 10442;
RX PubMed=11302791; DOI=10.1128/aac.45.5.1323-1336.2001;
RA Ito T., Katayama Y., Asada K., Mori N., Tsutsumimoto K.;
RT "Structural comparison of three types of staphylococcal cassette chromosome
RT mec integrated in the chromosome in methicillin-resistant Staphylococcus
RT aureus.";
RL Antimicrob. Agents Chemother. 45:1323-1336(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=CA05(JCSC1968), and JCSC1978(8/6-3P);
RX PubMed=11897611; DOI=10.1128/aac.46.4.1147-1152.2002;
RA Ma X.X., Ito T., Tiensasitorn C., Jamklang M., Chongtrakool P.,
RA Boyle-Vavra S., Daum R.S., Hiramatsu K.;
RT "Novel type of staphylococcal cassette chromosome mec identified in
RT community-acquired methicillin-resistant Staphylococcus aureus strains.";
RL Antimicrob. Agents Chemother. 46:1147-1152(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=MR108;
RX PubMed=12654286; DOI=10.1016/s1368-7646(03)00003-7;
RA Ito T., Okuma K., Ma X.X., Yuzawa H., Hiramatsu K.;
RT "Insights on antibiotic resistance of Staphylococcus aureus from its whole
RT genome: genomic island SCC.";
RL Drug Resist. Updat. 6:41-52(2003).
RN [5] {ECO:0007744|PDB:1VH0}
RP X-RAY CRYSTALLOGRAPHY (2.31 ANGSTROMS) OF 2-159.
RX PubMed=16021622; DOI=10.1002/prot.20541;
RA Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G.,
RA Buchanan S.G., Buchanan M.D., Batiyenko Y., Christopher J.A., Emtage S.,
RA Eroshkina A., Feil I., Furlong E.B., Gajiwala K.S., Gao X., He D.,
RA Hendle J., Huber A., Hoda K., Kearins P., Kissinger C., Laubert B.,
RA Lewis H.A., Lin J., Loomis K., Lorimer D., Louie G., Maletic M.,
RA Marsh C.D., Miller I., Molinari J., Muller-Dieckmann H.J., Newman J.M.,
RA Noland B.W., Pagarigan B., Park F., Peat T.S., Post K.W., Radojicic S.,
RA Ramos A., Romero R., Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J.,
RA Winhoven J., Wright T.A., Wu L., Xu J., Harris T.J.R.;
RT "Structural analysis of a set of proteins resulting from a bacterial
RT genomics project.";
RL Proteins 60:787-796(2005).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.31 ANGSTROMS) OF 2-159.
RX PubMed=16460560; DOI=10.1186/1471-2105-7-53;
RA von Grotthuss M., Plewczynski D., Ginalski K., Rychlewski L.,
RA Shakhnovich E.I.;
RT "PDB-UF: database of predicted enzymatic functions for unannotated protein
RT structures from structural genomics.";
RL BMC Bioinformatics 7:53-53(2006).
RN [7] {ECO:0007744|PDB:4FAK}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE, FUNCTION AS A METHYLTRANSFERASE, SUBUNIT, AND
RP MUTAGENESIS OF GLU-77.
RX PubMed=23150671; DOI=10.1074/jbc.m112.385138;
RA Boundy S., Safo M.K., Wang L., Musayev F.N., O'Farrell H.C., Rife J.P.,
RA Archer G.L.;
RT "Characterization of the Staphylococcus aureus rRNA methyltransferase
RT encoded by orfX, the gene containing the staphylococcal chromosome cassette
RT mec (SCCmec) insertion site.";
RL J. Biol. Chem. 288:132-140(2013).
CC -!- FUNCTION: Specifically methylates the pseudouridine at position 1915
CC (m3Psi1915) in 23S rRNA (By similarity). Specific for fully assembled
CC 70S ribosomes (PubMed:23150671). {ECO:0000255|HAMAP-Rule:MF_00658,
CC ECO:0000269|PubMed:23150671}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=pseudouridine(1915) in 23S rRNA + S-adenosyl-L-methionine =
CC H(+) + N(3)-methylpseudouridine(1915) in 23S rRNA + S-adenosyl-L-
CC homocysteine; Xref=Rhea:RHEA:42752, Rhea:RHEA-COMP:10221, Rhea:RHEA-
CC COMP:10222, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65314, ChEBI:CHEBI:74486; EC=2.1.1.177;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00658};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00658,
CC ECO:0000269|PubMed:23150671}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00658}.
CC -!- SIMILARITY: Belongs to the RNA methyltransferase RlmH family.
CC {ECO:0000255|HAMAP-Rule:MF_00658}.
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DR EMBL; AF181950; AAF85653.1; -; Genomic_DNA.
DR EMBL; D86934; BAA82243.1; -; Genomic_DNA.
DR EMBL; AB033763; BAA86653.1; -; Genomic_DNA.
DR EMBL; AB037671; BAB47681.1; -; Genomic_DNA.
DR EMBL; AB038513; BAC53844.1; -; Genomic_DNA.
DR EMBL; AB047089; BAC57492.1; -; Genomic_DNA.
DR EMBL; AB047239; BAB47141.1; -; Genomic_DNA.
DR EMBL; AB063172; BAB72121.1; -; Genomic_DNA.
DR EMBL; AB063173; BAB72138.1; -; Genomic_DNA.
DR EMBL; AB096217; BAC67575.1; -; Genomic_DNA.
DR RefSeq; WP_000704775.1; NZ_WYDB01000001.1.
DR PDB; 1VH0; X-ray; 2.31 A; A/B/C/D/E/F=2-159.
DR PDB; 4FAK; X-ray; 1.70 A; A=1-159.
DR PDBsum; 1VH0; -.
DR PDBsum; 4FAK; -.
DR AlphaFoldDB; P0C1V0; -.
DR SMR; P0C1V0; -.
DR GeneID; 66838363; -.
DR OMA; NEPYHHQ; -.
DR EvolutionaryTrace; P0C1V0; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0070038; F:rRNA (pseudouridine-N3-)-methyltransferase activity; IEA:UniProtKB-UniRule.
DR CDD; cd18081; RlmH-like; 1.
DR Gene3D; 3.40.1280.10; -; 1.
DR HAMAP; MF_00658; 23SrRNA_methyltr_H; 1.
DR InterPro; IPR029028; Alpha/beta_knot_MTases.
DR InterPro; IPR003742; RlmH-like.
DR InterPro; IPR029026; tRNA_m1G_MTases_N.
DR PANTHER; PTHR33603; PTHR33603; 1.
DR Pfam; PF02590; SPOUT_MTase; 1.
DR PIRSF; PIRSF004505; MT_bac; 1.
DR SUPFAM; SSF75217; SSF75217; 1.
DR TIGRFAMs; TIGR00246; tRNA_RlmH_YbeA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Methyltransferase; rRNA processing;
KW S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..159
FT /note="Ribosomal RNA large subunit methyltransferase H"
FT /id="PRO_0000198181"
FT BINDING 76
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00658,
FT ECO:0000269|PubMed:23150671, ECO:0007744|PDB:4FAK"
FT BINDING 108
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00658,
FT ECO:0000269|PubMed:23150671, ECO:0007744|PDB:4FAK"
FT BINDING 127..132
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00658,
FT ECO:0000269|PubMed:23150671, ECO:0007744|PDB:4FAK"
FT MUTAGEN 77
FT /note="E->A: 30% decrease in methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:23150671"
FT STRAND 2..9
FT /evidence="ECO:0007829|PDB:4FAK"
FT HELIX 14..27
FT /evidence="ECO:0007829|PDB:4FAK"
FT TURN 28..30
FT /evidence="ECO:0007829|PDB:4FAK"
FT STRAND 32..38
FT /evidence="ECO:0007829|PDB:4FAK"
FT HELIX 49..65
FT /evidence="ECO:0007829|PDB:4FAK"
FT STRAND 71..76
FT /evidence="ECO:0007829|PDB:4FAK"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:4FAK"
FT HELIX 85..97
FT /evidence="ECO:0007829|PDB:4FAK"
FT STRAND 102..107
FT /evidence="ECO:0007829|PDB:4FAK"
FT HELIX 115..120
FT /evidence="ECO:0007829|PDB:4FAK"
FT STRAND 122..127
FT /evidence="ECO:0007829|PDB:4FAK"
FT HELIX 134..153
FT /evidence="ECO:0007829|PDB:4FAK"
SQ SEQUENCE 159 AA; 18306 MW; 8B38405E61012716 CRC64;
MKITILAVGK LKEKYWKQAI AEYEKRLGPY TKIDIIEVPD EKAPENMSDK EIEQVKEKEG
QRILAKIKPQ STVITLEIQG KMLSSEGLAQ ELNQRMTQGQ SDFVFVIGGS NGLHKDVLQR
SNYALSFSKM TFPHQMMRVV LIEQVYRAFK IMRGEAYHK
