ID NPMA_ECOLX Reviewed; 219 AA.
AC A8C927;
DT 16-MAY-2012, integrated into UniProtKB/Swiss-Prot.
DT 13-NOV-2007, sequence version 1.
DT 27-MAR-2024, entry version 54.
DE RecName: Full=16S rRNA (adenine(1408)-N(1))-methyltransferase;
DE EC=2.1.1.180;
DE AltName: Full=16S rRNA m1A1408 methyltransferase;
GN Name=npmA;
OS Escherichia coli.
OG Plasmid pARS3.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=562;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-5, FUNCTION, AND
RP CATALYTIC ACTIVITY.
RC STRAIN=ARS3;
RX PubMed=17875999; DOI=10.1128/aac.00926-07;
RA Wachino J., Shibayama K., Kurokawa H., Kimura K., Yamane K., Suzuki S.,
RA Shibata N., Ike Y., Arakawa Y.;
RT "Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in
RT a clinically isolated Escherichia coli strain resistant to structurally
RT diverse aminoglycosides.";
RL Antimicrob. Agents Chemother. 51:4401-4409(2007).
RN [2]
RP FUNCTION, AND CRYSTALLIZATION.
RX PubMed=20667473; DOI=10.1016/j.pep.2010.07.005;
RA Zelinskaya N., Rankin C.R., Macmaster R., Savic M., Conn G.L.;
RT "Expression, purification and crystallization of adenosine 1408
RT aminoglycoside-resistance rRNA methyltransferases for structural studies.";
RL Protein Expr. Purif. 75:89-94(2011).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-METHIONINE.
RX PubMed=20639535; DOI=10.1093/nar/gkq627;
RA Macmaster R., Zelinskaya N., Savic M., Rankin C.R., Conn G.L.;
RT "Structural insights into the function of aminoglycoside-resistance A1408
RT 16S rRNA methyltransferases from antibiotic-producing and human pathogenic
RT bacteria.";
RL Nucleic Acids Res. 38:7791-7799(2010).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE AND S-ADENOSYL-L-METHIONINE, FUNCTION AS A
RP METHYLTRANSFERASE, AND MUTAGENESIS OF ASP-30; ASP-55; GLU-88; PRO-106;
RP TRP-107; THR-109; PHE-177; SER-195; TRP-197; LYS-199; ARG-200 AND ARG-205.
RX PubMed=21062819; DOI=10.1093/nar/gkq1033;
RA Husain N., Obranic S., Koscinski L., Seetharaman J., Babic F.,
RA Bujnicki J.M., Maravic-Vlahovicek G., Sivaraman J.;
RT "Structural basis for the methylation of A1408 in 16S rRNA by a
RT panaminoglycoside resistance methyltransferase NpmA from a clinical isolate
RT and analysis of the NpmA interactions with the 30S ribosomal subunit.";
RL Nucleic Acids Res. 39:1903-1918(2011).
CC -!- FUNCTION: Specifically methylates the N(1) position of adenine 1408 in
CC 16S rRNA. Confers resistance to various aminoglycosides, including
CC kanamycin, neomycin, apramycin, ribostamycin and gentamicin. Methylates
CC only fully assembled 30S subunits. {ECO:0000269|PubMed:17875999,
CC ECO:0000269|PubMed:20667473, ECO:0000269|PubMed:21062819}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=adenosine(1408) in 16S rRNA + S-adenosyl-L-methionine = H(+) +
CC N(1)-methyladenosine(1408) in 16S rRNA + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42776, Rhea:RHEA-COMP:10227, Rhea:RHEA-COMP:10228,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:74411, ChEBI:CHEBI:74491; EC=2.1.1.180;
CC Evidence={ECO:0000269|PubMed:17875999};
CC -!- SIMILARITY: Belongs to the methyltransferase superfamily. Kanamycin-
CC apramycin resistance family. {ECO:0000305}.
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DR EMBL; AB261016; BAF80809.1; -; Genomic_DNA.
DR RefSeq; WP_032492089.1; NG_048018.1.
DR PDB; 3MTE; X-ray; 1.80 A; A/B=1-219.
DR PDB; 3P2E; X-ray; 1.68 A; A/B=1-219.
DR PDB; 3P2I; X-ray; 2.40 A; A/B=1-219.
DR PDB; 3P2K; X-ray; 2.70 A; A/B/C/D=1-219.
DR PDB; 3PB3; X-ray; 1.90 A; A/B=1-219.
DR PDB; 4OX9; X-ray; 3.80 A; Y=1-219.
DR PDBsum; 3MTE; -.
DR PDBsum; 3P2E; -.
DR PDBsum; 3P2I; -.
DR PDBsum; 3P2K; -.
DR PDBsum; 3PB3; -.
DR PDBsum; 4OX9; -.
DR AlphaFoldDB; A8C927; -.
DR SMR; A8C927; -.
DR KEGG; ag:BAF80809; -.
DR BRENDA; 2.1.1.180; 2026.
DR EvolutionaryTrace; A8C927; -.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.150; Vaccinia Virus protein VP39; 1.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR SUPFAM; SSF53335; S-adenosyl-L-methionine-dependent methyltransferases; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic resistance; Direct protein sequencing;
KW Methyltransferase; Plasmid; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..219
FT /note="16S rRNA (adenine(1408)-N(1))-methyltransferase"
FT /id="PRO_0000417015"
FT BINDING 32
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:20639535,
FT ECO:0000269|PubMed:21062819"
FT BINDING 38
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:20639535,
FT ECO:0000269|PubMed:21062819"
FT BINDING 55
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000269|PubMed:20639535,
FT ECO:0000269|PubMed:21062819"
FT BINDING 87..88
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 104..109
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 195..197
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT MUTAGEN 30
FT /note="D->A: Loss of kanamycin resistance. Strong decrease
FT in methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 55
FT /note="D->A: Decrease in kanamycin resistance. Decrease in
FT methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 88
FT /note="E->A: No change in kanamycin resistance."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 106
FT /note="P->A: No change in kanamycin resistance. Decrease in
FT methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 107
FT /note="W->A: Loss of kanamycin resistance. Strong decrease
FT in methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 109
FT /note="T->A: No change in kanamycin resistance."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 177
FT /note="F->A: No change in kanamycin resistance. Decrease in
FT methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 195
FT /note="S->A: No change in kanamycin resistance."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 197
FT /note="W->A: Loss of kanamycin resistance. Strong decrease
FT in methyltransferase activity."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 199
FT /note="K->A: No change in kanamycin resistance."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 200
FT /note="R->A: No change in kanamycin resistance."
FT /evidence="ECO:0000269|PubMed:21062819"
FT MUTAGEN 205
FT /note="R->A: No change in kanamycin resistance."
FT /evidence="ECO:0000269|PubMed:21062819"
FT STRAND 3..5
FT /evidence="ECO:0007829|PDB:3P2E"
FT STRAND 8..10
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 14..21
FT /evidence="ECO:0007829|PDB:3P2E"
FT STRAND 25..31
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 37..44
FT /evidence="ECO:0007829|PDB:3P2E"
FT STRAND 49..54
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 59..61
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 62..68
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:3P2E"
FT STRAND 78..83
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:3MTE"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:3P2E"
FT STRAND 98..105
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 108..115
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 119..126
FT /evidence="ECO:0007829|PDB:3P2E"
FT STRAND 129..139
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 144..152
FT /evidence="ECO:0007829|PDB:3MTE"
FT HELIX 160..164
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 166..174
FT /evidence="ECO:0007829|PDB:3P2E"
FT STRAND 178..185
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 187..190
FT /evidence="ECO:0007829|PDB:3P2E"
FT HELIX 196..203
FT /evidence="ECO:0007829|PDB:3P2E"
FT STRAND 209..215
FT /evidence="ECO:0007829|PDB:3P2E"
SQ SEQUENCE 219 AA; 24887 MW; 0E03149FDBF9870A CRC64;
MLILKGTKTV DLSKDELTEI IGQFDRVHID LGTGDGRNIY KLAINDQNTF YIGIDPVKEN
LFDISKKIIK KPSKGGLSNV VFVIAAAESL PFELKNIADS ISILFPWGTL LEYVIKPNRD
ILSNVADLAK KEAHFEFVTT YSDSYEEAEI KKRGLPLLSK AYFLSEQYKA ELSNSGFRID
DVKELDNEYV KQFNSLWAKR LAFGRKRSFF RVSGHVSKH
//
