› 4ox9

X-ray diffraction
3.8Å resolution

Crystal structure of the aminoglycoside resistance methyltransferase NpmA bound to the 30S ribosomal subunit

Released:
DOI: 10.2210/pdb4ox9/pdb
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PDB entry 4ox9 coloured by chain, front view.
PDB entry 4ox9 coloured by chain, side view.
PDB entry 4ox9 coloured by chain, top view.
Source organisms:
Primary publication:
Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA.
Dunkle JA, Vinal K, Desai PM, Zelinskaya N, Savic M, West DM, Conn GL, Dunham CM
Proc Natl Acad Sci U S A 111 6275-80 (2014)
PMID: 24717845

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + adenine(1408) in 16S rRNA = S-adenosyl-L-homocysteine + N(1)-methyladenine(1408) in 16S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 22-mer (preferred)
PDBe Complex ID:
PDB-CPX-289199 (preferred)
Entry contents:
21 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (22 distinct):
Small ribosomal subunit protein uS2 Chain: B
Molecule details ›
Chain: B
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Structure domains:
Small ribosomal subunit protein uS3 Chain: C
Molecule details ›
Chain: C
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Structure domains:
Small ribosomal subunit protein uS4 Chain: D
Small ribosomal subunit protein uS5 Chain: E
Small ribosomal subunit protein bS6 Chain: F
Small ribosomal subunit protein uS7 Chain: G
30S ribosomal protein S8 Chain: H
Small ribosomal subunit protein uS9 Chain: I
Small ribosomal subunit protein uS10 Chain: J
Small ribosomal subunit protein uS11 Chain: K
Small ribosomal subunit protein uS12 Chain: L
Small ribosomal subunit protein uS13 Chain: M
30S ribosomal protein S14 type Z Chain: N
Small ribosomal subunit protein uS15 Chain: O
Small ribosomal subunit protein bS16 Chain: P
30S ribosomal protein S17 Chain: Q
Small ribosomal subunit protein bS18 Chain: R
Small ribosomal subunit protein uS19 Chain: S
Small ribosomal subunit protein bS20 Chain: T
Small ribosomal subunit protein bTHX Chain: V
16S rRNA (adenine(1408)-N(1))-methyltransferase Chain: Y
16S ribosomal RNA Chain: A

Ligands and Environments


Cofactor: Ligand SFG 1 x SFG
2 bound ligands:
Ligand MG 120 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P41212
Unit cell:
a: 403.52Å b: 403.52Å c: 176.61Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.233 0.257
Expression system: Escherichia coli

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Citations

8 review citations

Aminoglycoside Resistance: The Emergence of Acquired 16S Ribosomal RNA Methyltransferases.
Doi et al. (2016)
7 more

10 mentions without citation

Mechanisms of Resistance to Aminoglycoside Antibiotics: Overview and Perspectives.
Garneau-Tsodikova et al. (2016)
9 more

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