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Protein

16S rRNA (adenine(1408)-N(1))-methyltransferase

Gene

npmA

Organism
Escherichia coli
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Specifically methylates the N1 position of adenine 1408 in 16S rRNA. Confers resistance to various aminoglycosides, including kanamycin, neomycin, apramycin, ribostamycin and gentamicin. Methylates only fully assembled 30S subunits.3 Publications

Catalytic activityi

S-adenosyl-L-methionine + adenine(1408) in 16S rRNA = S-adenosyl-L-homocysteine + N(1)-methyladenine(1408) in 16S rRNA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei32 – 321S-adenosyl-L-methionine; via carbonyl oxygen2 Publications
Binding sitei38 – 381S-adenosyl-L-methionine2 Publications
Binding sitei55 – 551S-adenosyl-L-methionine2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Antibiotic resistance

Keywords - Ligandi

S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.180. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
16S rRNA (adenine(1408)-N(1))-methyltransferase (EC:2.1.1.180)
Alternative name(s):
16S rRNA m1A1408 methyltransferase
Gene namesi
Name:npmA
Encoded oniPlasmid pARS30 Publication
OrganismiEscherichia coli
Taxonomic identifieri562 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi30 – 301D → A: Loss of kanamycin resistance. Strong decrease in methyltransferase activity. 1 Publication
Mutagenesisi55 – 551D → A: Decrease in kanamycin resistance. Decrease in methyltransferase activity. 1 Publication
Mutagenesisi88 – 881E → A: No change in kanamycin resistance. 1 Publication
Mutagenesisi106 – 1061P → A: No change in kanamycin resistance. Decrease in methyltransferase activity. 1 Publication
Mutagenesisi107 – 1071W → A: Loss of kanamycin resistance. Strong decrease in methyltransferase activity. 1 Publication
Mutagenesisi109 – 1091T → A: No change in kanamycin resistance. 1 Publication
Mutagenesisi177 – 1771F → A: No change in kanamycin resistance. Decrease in methyltransferase activity. 1 Publication
Mutagenesisi195 – 1951S → A: No change in kanamycin resistance. 1 Publication
Mutagenesisi197 – 1971W → A: Loss of kanamycin resistance. Strong decrease in methyltransferase activity. 1 Publication
Mutagenesisi199 – 1991K → A: No change in kanamycin resistance. 1 Publication
Mutagenesisi200 – 2001R → A: No change in kanamycin resistance. 1 Publication
Mutagenesisi205 – 2051R → A: No change in kanamycin resistance. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 21921916S rRNA (adenine(1408)-N(1))-methyltransferasePRO_0000417015Add
BLAST

Structurei

Secondary structure

1
219
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 53Combined sources
Beta strandi8 – 103Combined sources
Helixi14 – 218Combined sources
Beta strandi25 – 317Combined sources
Helixi37 – 448Combined sources
Beta strandi49 – 546Combined sources
Helixi59 – 613Combined sources
Helixi62 – 687Combined sources
Helixi72 – 743Combined sources
Beta strandi78 – 836Combined sources
Helixi87 – 893Combined sources
Helixi92 – 943Combined sources
Beta strandi98 – 1058Combined sources
Helixi108 – 1158Combined sources
Helixi119 – 1268Combined sources
Beta strandi129 – 13911Combined sources
Helixi144 – 1529Combined sources
Helixi160 – 1645Combined sources
Helixi166 – 1749Combined sources
Beta strandi178 – 1858Combined sources
Helixi187 – 1904Combined sources
Helixi196 – 2038Combined sources
Beta strandi209 – 2157Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3MTEX-ray1.80A/B1-219[»]
3P2EX-ray1.68A/B1-219[»]
3P2IX-ray2.40A/B1-219[»]
3P2KX-ray2.70A/B/C/D1-219[»]
3PB3X-ray1.90A/B1-219[»]
4OX9X-ray3.80Y1-219[»]
ProteinModelPortaliA8C927.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiA8C927.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni87 – 882S-adenosyl-L-methionine binding
Regioni104 – 1096S-adenosyl-L-methionine binding
Regioni195 – 1973S-adenosyl-L-methionine binding

Sequence similaritiesi

Phylogenomic databases

KOiK18846.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR029063. SAM-dependent_MTases.
IPR003358. tRNA_(Gua-N-7)_MeTrfase_Trmb.
[Graphical view]
PfamiPF02390. Methyltransf_4. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.

Sequencei

Sequence statusi: Complete.

A8C927-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLILKGTKTV DLSKDELTEI IGQFDRVHID LGTGDGRNIY KLAINDQNTF
60 70 80 90 100
YIGIDPVKEN LFDISKKIIK KPSKGGLSNV VFVIAAAESL PFELKNIADS
110 120 130 140 150
ISILFPWGTL LEYVIKPNRD ILSNVADLAK KEAHFEFVTT YSDSYEEAEI
160 170 180 190 200
KKRGLPLLSK AYFLSEQYKA ELSNSGFRID DVKELDNEYV KQFNSLWAKR
210
LAFGRKRSFF RVSGHVSKH
Length:219
Mass (Da):24,887
Last modified:November 13, 2007 - v1
Checksum:i0E03149FDBF9870A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB261016 Genomic DNA. Translation: BAF80809.1.

Genome annotation databases

KEGGiag:BAF80809.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB261016 Genomic DNA. Translation: BAF80809.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3MTEX-ray1.80A/B1-219[»]
3P2EX-ray1.68A/B1-219[»]
3P2IX-ray2.40A/B1-219[»]
3P2KX-ray2.70A/B/C/D1-219[»]
3PB3X-ray1.90A/B1-219[»]
4OX9X-ray3.80Y1-219[»]
ProteinModelPortaliA8C927.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGiag:BAF80809.

Phylogenomic databases

KOiK18846.

Enzyme and pathway databases

BRENDAi2.1.1.180. 2026.

Miscellaneous databases

EvolutionaryTraceiA8C927.

Family and domain databases

Gene3Di3.40.50.150. 1 hit.
InterProiIPR029063. SAM-dependent_MTases.
IPR003358. tRNA_(Gua-N-7)_MeTrfase_Trmb.
[Graphical view]
PfamiPF02390. Methyltransf_4. 1 hit.
[Graphical view]
SUPFAMiSSF53335. SSF53335. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides."
    Wachino J., Shibayama K., Kurokawa H., Kimura K., Yamane K., Suzuki S., Shibata N., Ike Y., Arakawa Y.
    Antimicrob. Agents Chemother. 51:4401-4409(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-5, FUNCTION, CATALYTIC ACTIVITY.
    Strain: ARS3.
  2. "Expression, purification and crystallization of adenosine 1408 aminoglycoside-resistance rRNA methyltransferases for structural studies."
    Zelinskaya N., Rankin C.R., Macmaster R., Savic M., Conn G.L.
    Protein Expr. Purif. 75:89-94(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CRYSTALLIZATION.
  3. "Structural insights into the function of aminoglycoside-resistance A1408 16S rRNA methyltransferases from antibiotic-producing and human pathogenic bacteria."
    Macmaster R., Zelinskaya N., Savic M., Rankin C.R., Conn G.L.
    Nucleic Acids Res. 38:7791-7799(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE.
  4. "Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit."
    Husain N., Obranic S., Koscinski L., Seetharaman J., Babic F., Bujnicki J.M., Maravic-Vlahovicek G., Sivaraman J.
    Nucleic Acids Res. 39:1903-1918(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS) IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE AND S-ADENOSYL-L-METHIONINE, FUNCTION AS A METHYLTRANSFERASE, MUTAGENESIS OF ASP-30; ASP-55; GLU-88; PRO-106; TRP-107; THR-109; PHE-177; SER-195; TRP-197; LYS-199; ARG-200 AND ARG-205.

Entry informationi

Entry nameiNPMA_ECOLX
AccessioniPrimary (citable) accession number: A8C927
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2012
Last sequence update: November 13, 2007
Last modified: May 11, 2016
This is version 34 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing, Plasmid

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.