4OX9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Molecular recognition and modification of the 30S ribosome by the aminoglycoside-resistance methyltransferase NpmA.

Dunkle, J.A.Vinal, K.Desai, P.M.Zelinskaya, N.Savic, M.West, D.M.Conn, G.L.Dunham, C.M.

(2014) Proc Natl Acad Sci U S A 111: 6275-6280

  • DOI: 10.1073/pnas.1402789111
  • Primary Citation of Related Structures:  
    4OX9

  • PubMed Abstract: 
  • Aminoglycosides are potent, broad spectrum, ribosome-targeting antibacterials whose clinical efficacy is seriously threatened by multiple resistance mechanisms. Here, we report the structural basis for 30S recognition by the novel plasmid-mediated aminoglycoside-resistance rRNA methyltransferase A (NpmA) ...

    Aminoglycosides are potent, broad spectrum, ribosome-targeting antibacterials whose clinical efficacy is seriously threatened by multiple resistance mechanisms. Here, we report the structural basis for 30S recognition by the novel plasmid-mediated aminoglycoside-resistance rRNA methyltransferase A (NpmA). These studies are supported by biochemical and functional assays that define the molecular features necessary for NpmA to catalyze m(1)A1408 modification and confer resistance. The requirement for the mature 30S as a substrate for NpmA is clearly explained by its recognition of four disparate 16S rRNA helices brought into proximity by 30S assembly. Our structure captures a "precatalytic state" in which multiple structural reorganizations orient functionally critical residues to flip A1408 from helix 44 and position it precisely in a remodeled active site for methylation. Our findings provide a new molecular framework for the activity of aminoglycoside-resistance rRNA methyltransferases that may serve as a functional paradigm for other modification enzymes acting late in 30S biogenesis.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E161Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J104Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L131Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q104Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S92Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth V]26Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
16S rRNA (adenine(1408)-N(1))-methyltransferaseV [auth Y]222Escherichia coliMutation(s): 0 
Gene Names: npmA
EC: 2.1.1.180
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1513Thermus thermophilus
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SFG (Subject of Investigation/LOI)
Query on SFG

Download Ideal Coordinates CCD File 
OE [auth Y]SINEFUNGIN
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
KE [auth D], ME [auth N]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A] , AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , BA [auth A] , BB [auth A] , BC [auth A] , 
AA [auth A],  AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  BA [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  CA [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  DA [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  EA [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  IA [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth B],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth E],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth N],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  W [auth A],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  X [auth A],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  Y [auth A],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  Z [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 403.52α = 90
b = 403.52β = 90
c = 176.61γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references
  • Version 1.2: 2014-05-21
    Changes: Data collection
  • Version 1.3: 2014-10-01
    Changes: Database references
  • Version 1.4: 2015-09-30
    Changes: Data collection