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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)DescriptionActionsGraphical viewLength
Binding sitei32S-adenosyl-L-methionine; via carbonyl oxygen2 Publications1
Binding sitei38S-adenosyl-L-methionine2 Publications1
Binding sitei55S-adenosyl-L-methionine2 Publications1

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi30D → A: Loss of kanamycin resistance. Strong decrease in methyltransferase activity. 1 Publication1
Mutagenesisi55D → A: Decrease in kanamycin resistance. Decrease in methyltransferase activity. 1 Publication1
Mutagenesisi88E → A: No change in kanamycin resistance. 1 Publication1
Mutagenesisi106P → A: No change in kanamycin resistance. Decrease in methyltransferase activity. 1 Publication1
Mutagenesisi107W → A: Loss of kanamycin resistance. Strong decrease in methyltransferase activity. 1 Publication1
Mutagenesisi109T → A: No change in kanamycin resistance. 1 Publication1
Mutagenesisi177F → A: No change in kanamycin resistance. Decrease in methyltransferase activity. 1 Publication1
Mutagenesisi195S → A: No change in kanamycin resistance. 1 Publication1
Mutagenesisi197W → A: Loss of kanamycin resistance. Strong decrease in methyltransferase activity. 1 Publication1
Mutagenesisi199K → A: No change in kanamycin resistance. 1 Publication1
Mutagenesisi200R → A: No change in kanamycin resistance. 1 Publication1
Mutagenesisi205R → A: No change in kanamycin resistance. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004170151 – 21916S rRNA (adenine(1408)-N(1))-methyltransferaseAdd BLAST219

Structurei

Secondary structure

1219
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 5Combined sources3
Beta strandi8 – 10Combined sources3
Helixi14 – 21Combined sources8
Beta strandi25 – 31Combined sources7
Helixi37 – 44Combined sources8
Beta strandi49 – 54Combined sources6
Helixi59 – 61Combined sources3
Helixi62 – 68Combined sources7
Helixi72 – 74Combined sources3
Beta strandi78 – 83Combined sources6
Helixi87 – 89Combined sources3
Helixi92 – 94Combined sources3
Beta strandi98 – 105Combined sources8
Helixi108 – 115Combined sources8
Helixi119 – 126Combined sources8
Beta strandi129 – 139Combined sources11
Helixi144 – 152Combined sources9
Helixi160 – 164Combined sources5
Helixi166 – 174Combined sources9
Beta strandi178 – 185Combined sources8
Helixi187 – 190Combined sources4
Helixi196 – 203Combined sources8
Beta strandi209 – 215Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
SMRiA8C927.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiA8C927.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni87 – 88S-adenosyl-L-methionine binding2
Regioni104 – 109S-adenosyl-L-methionine binding6
Regioni195 – 197S-adenosyl-L-methionine binding3

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.
RefSeqiWP_032492089.1. NG_048018.1.

Genome annotation databases

KEGGiag:BAF80809.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB261016 Genomic DNA. Translation: BAF80809.1.
RefSeqiWP_032492089.1. NG_048018.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
SMRiA8C927.
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...

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: November 2, 2016
This is version 36 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.