RLMH_ECOLI
ID RLMH_ECOLI Reviewed; 155 AA.
AC P0A8I8; P05850;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Ribosomal RNA large subunit methyltransferase H {ECO:0000255|HAMAP-Rule:MF_00658, ECO:0000305};
DE EC=2.1.1.177 {ECO:0000255|HAMAP-Rule:MF_00658, ECO:0000269|PubMed:18755835, ECO:0000269|PubMed:18755836, ECO:0000269|PubMed:20817755, ECO:0000269|PubMed:28428565};
DE AltName: Full=23S rRNA (pseudouridine1915-N3)-methyltransferase {ECO:0000255|HAMAP-Rule:MF_00658, ECO:0000305};
DE AltName: Full=23S rRNA m3Psi1915 methyltransferase {ECO:0000255|HAMAP-Rule:MF_00658, ECO:0000305};
DE AltName: Full=rRNA (pseudouridine-N3-)-methyltransferase RlmH {ECO:0000255|HAMAP-Rule:MF_00658, ECO:0000305};
GN Name=rlmH {ECO:0000255|HAMAP-Rule:MF_00658, ECO:0000303|PubMed:18755835,
GN ECO:0000303|PubMed:18755836}; Synonyms=ybeA;
GN OrderedLocusNames=b0636, JW0631;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=3533535; DOI=10.1111/j.1432-1033.1986.tb09961.x;
RA Asoh S., Matsuzawa H., Ishino F., Strominger J.L., Matsuhashi M., Ohta T.;
RT "Nucleotide sequence of the pbpA gene and characteristics of the deduced
RT amino acid sequence of penicillin-binding protein 2 of Escherichia coli
RT K12.";
RL Eur. J. Biochem. 160:231-238(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP FUNCTION AS A METHYLTRANSFERASE, AND CATALYTIC ACTIVITY.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=18755836; DOI=10.1261/rna.1186608;
RA Ero R., Peil L., Liiv A., Remme J.;
RT "Identification of pseudouridine methyltransferase in Escherichia coli.";
RL RNA 14:2223-2233(2008).
RN [7]
RP FUNCTION AS A METHYLTRANSFERASE, CATALYTIC ACTIVITY, AND 3D-STRUCTURE
RP MODELING.
RX PubMed=18755835; DOI=10.1261/rna.1198108;
RA Purta E., Kaminska K.H., Kasprzak J.M., Bujnicki J.M., Douthwaite S.;
RT "YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in
RT 23S rRNA.";
RL RNA 14:2234-2244(2008).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=20817755; DOI=10.1261/rna.2234310;
RA Ero R., Leppik M., Liiv A., Remme J.;
RT "Specificity and kinetics of 23S rRNA modification enzymes RlmH and RluD.";
RL RNA 16:2075-2084(2010).
RN [9] {ECO:0007744|PDB:1NS5}
RP X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS), AND SUBUNIT.
RG Northeast structural genomics consortium (NESG);
RT "Structure of ybeA from E.coli.";
RL Submitted (JAN-2005) to the PDB data bank.
RN [10] {ECO:0007744|PDB:5TWJ, ECO:0007744|PDB:5TWK}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 2-155 IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, SUBUNIT, AND MUTAGENESIS OF HIS-129; GLU-138; ARG-142; TYR-152;
RP HIS-153 AND ARG-154.
RX PubMed=28428565; DOI=10.1038/s41598-017-01186-5;
RA Koh C.S., Madireddy R., Beane T.J., Zamore P.D., Korostelev A.A.;
RT "Small methyltransferase RlmH assembles a composite active site to
RT methylate a ribosomal pseudouridine.";
RL Sci. Rep. 7:969-969(2017).
CC -!- FUNCTION: Specifically methylates the pseudouridine at position 1915
CC (m3Psi1915) in 23S rRNA. Specific for fully assembled 70S ribosomes.
CC {ECO:0000269|PubMed:18755835, ECO:0000269|PubMed:18755836,
CC ECO:0000269|PubMed:20817755, ECO:0000269|PubMed:28428565}.
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 ECO:0000269|PubMed:18755835, ECO:0000269|PubMed:18755836,
CC ECO:0000269|PubMed:20817755, ECO:0000269|PubMed:28428565};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.51 uM for 70S ribosome {ECO:0000269|PubMed:20817755};
CC KM=0.3 uM for 70S ribosome {ECO:0000269|PubMed:28428565};
CC KM=27 uM for S-adenosyl-L-methionine {ECO:0000269|PubMed:20817755};
CC Note=kcat is 5-6 min(-1) (PubMed:20817755). kcat is 2.5 min(-1)
CC (PubMed:28428565). {ECO:0000269|PubMed:20817755,
CC ECO:0000269|PubMed:28428565};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00658,
CC ECO:0000269|PubMed:28428565, ECO:0000269|Ref.9}.
CC -!- INTERACTION:
CC P0A8I8; P0A7V0: rpsB; NbExp=2; IntAct=EBI-560148, EBI-543439;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00658,
CC ECO:0000305}.
CC -!- SIMILARITY: Belongs to the RNA methyltransferase RlmH family.
CC {ECO:0000255|HAMAP-Rule:MF_00658, ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; X04516; CAA28200.1; -; Genomic_DNA.
DR EMBL; U82598; AAB40836.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73737.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35283.1; -; Genomic_DNA.
DR PIR; B24995; QQECP1.
DR RefSeq; NP_415169.1; NC_000913.3.
DR RefSeq; WP_000776104.1; NZ_STEB01000031.1.
DR PDB; 1NS5; X-ray; 1.68 A; A/B=1-155.
DR PDB; 5TWJ; X-ray; 2.30 A; A/B/C/D=2-155.
DR PDB; 5TWK; X-ray; 2.10 A; A/B/C/D=2-155.
DR PDB; 5ZYO; X-ray; 1.75 A; A/B/C/D=1-155.
DR PDB; 7CEM; X-ray; 2.43 A; A/B=1-155.
DR PDB; 7CF7; X-ray; 1.62 A; A/B=1-155.
DR PDB; 7CFY; X-ray; 2.41 A; A/B/C/D=1-155.
DR PDBsum; 1NS5; -.
DR PDBsum; 5TWJ; -.
DR PDBsum; 5TWK; -.
DR PDBsum; 5ZYO; -.
DR PDBsum; 7CEM; -.
DR PDBsum; 7CF7; -.
DR PDBsum; 7CFY; -.
DR AlphaFoldDB; P0A8I8; -.
DR SMR; P0A8I8; -.
DR BioGRID; 4259479; 46.
DR DIP; DIP-11357N; -.
DR IntAct; P0A8I8; 11.
DR STRING; 511145.b0636; -.
DR jPOST; P0A8I8; -.
DR PaxDb; P0A8I8; -.
DR PRIDE; P0A8I8; -.
DR EnsemblBacteria; AAC73737; AAC73737; b0636.
DR EnsemblBacteria; BAA35283; BAA35283; BAA35283.
DR GeneID; 67416322; -.
DR GeneID; 945239; -.
DR KEGG; ecj:JW0631; -.
DR KEGG; eco:b0636; -.
DR PATRIC; fig|1411691.4.peg.1632; -.
DR EchoBASE; EB1234; -.
DR eggNOG; COG1576; Bacteria.
DR HOGENOM; CLU_100552_1_0_6; -.
DR InParanoid; P0A8I8; -.
DR OMA; NEPYHHQ; -.
DR PhylomeDB; P0A8I8; -.
DR BioCyc; EcoCyc:EG11254-MON; -.
DR BioCyc; MetaCyc:EG11254-MON; -.
DR BRENDA; 2.1.1.177; 2026.
DR EvolutionaryTrace; P0A8I8; -.
DR PRO; PR:P0A8I8; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IC:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; NAS:UniProtKB.
DR GO; GO:0043022; F:ribosome binding; NAS:UniProtKB.
DR GO; GO:0070038; F:rRNA (pseudouridine-N3-)-methyltransferase activity; IDA:EcoCyc.
DR GO; GO:0070475; P:rRNA base methylation; IMP:EcoCyc.
DR GO; GO:0031167; P:rRNA methylation; IDA:UniProtKB.
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; Reference proteome;
KW rRNA processing; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..155
FT /note="Ribosomal RNA large subunit methyltransferase H"
FT /id="PRO_0000198115"
FT BINDING 72
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00658,
FT ECO:0000269|PubMed:28428565, ECO:0007744|PDB:5TWJ"
FT BINDING 103
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00658,
FT ECO:0000269|PubMed:28428565, ECO:0007744|PDB:5TWJ"
FT BINDING 122..127
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00658,
FT ECO:0000269|PubMed:28428565, ECO:0007744|PDB:5TWJ"
FT MUTAGEN 129
FT /note="H->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:28428565"
FT MUTAGEN 138
FT /note="E->A,Q: Loss of activity."
FT /evidence="ECO:0000269|PubMed:28428565"
FT MUTAGEN 142
FT /note="R->A: Decrease in activity."
FT /evidence="ECO:0000269|PubMed:28428565"
FT MUTAGEN 152
FT /note="Y->F: Loss of activity."
FT /evidence="ECO:0000269|PubMed:28428565"
FT MUTAGEN 153
FT /note="H->F: Loss of activity."
FT /evidence="ECO:0000269|PubMed:28428565"
FT MUTAGEN 154
FT /note="R->A: Loss of activity. Impairs ribosome binding."
FT /evidence="ECO:0000269|PubMed:28428565"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:1NS5"
FT HELIX 14..24
FT /evidence="ECO:0007829|PDB:1NS5"
FT STRAND 33..38
FT /evidence="ECO:0007829|PDB:1NS5"
FT STRAND 45..47
FT /evidence="ECO:0007829|PDB:5TWJ"
FT HELIX 49..64
FT /evidence="ECO:0007829|PDB:1NS5"
FT STRAND 67..72
FT /evidence="ECO:0007829|PDB:1NS5"
FT HELIX 81..94
FT /evidence="ECO:0007829|PDB:7CF7"
FT STRAND 98..102
FT /evidence="ECO:0007829|PDB:7CF7"
FT HELIX 110..115
FT /evidence="ECO:0007829|PDB:7CF7"
FT STRAND 117..121
FT /evidence="ECO:0007829|PDB:7CF7"
FT HELIX 122..124
FT /evidence="ECO:0007829|PDB:7CF7"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:7CF7"
FT HELIX 132..145
FT /evidence="ECO:0007829|PDB:7CF7"
FT STRAND 147..150
FT /evidence="ECO:0007829|PDB:7CEM"
FT HELIX 151..153
FT /evidence="ECO:0007829|PDB:5TWK"
SQ SEQUENCE 155 AA; 17341 MW; DFA0EFCF4EB057E7 CRC64;
MKLQLVAVGT KMPDWVQTGF TEYLRRFPKD MPFELIEIPA GKRGKNADIK RILDKEGEQM
LAAAGKNRIV TLDIPGKPWD TPQLAAELER WKLDGRDVSL LIGGPEGLSP ACKAAAEQSW
SLSALTLPHP LVRVLVAESL YRAWSITTNH PYHRE
