4WWW

Crystal structure of the E. coli ribosome bound to CEM-101


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report



Literature

Binding and action of CEM-101, a new fluoroketolide antibiotic that inhibits protein synthesis.

Llano-Sotelo, B.Dunkle, J.Klepacki, D.Zhang, W.Fernandes, P.Cate, J.H.Mankin, A.S.

(2010) Antimicrob Agents Chemother 54: 4961-4970

  • DOI: 10.1128/AAC.00860-10
  • Primary Citation of Related Structures:  
    4WWW

  • PubMed Abstract: 
  • We characterized the mechanism of action and the drug-binding site of a novel ketolide, CEM-101, which belongs to the latest class of macrolide antibiotics. CEM-101 shows high affinity for the ribosomes of Gram-negative (Escherichia coli) and Gram-po ...

    We characterized the mechanism of action and the drug-binding site of a novel ketolide, CEM-101, which belongs to the latest class of macrolide antibiotics. CEM-101 shows high affinity for the ribosomes of Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria. The ketolide shows high selectivity in its inhibitory action and readily interferes with synthesis of a reporter protein in the bacterial but not eukaryotic cell-free translation system. Binding of CEM-101 to its ribosomal target site was characterized biochemically and by X-ray crystallography. The X-ray structure of CEM-101 in complex with the E. coli ribosome shows that the drug binds in the major macrolide site in the upper part of the ribosomal exit tunnel. The lactone ring of the drug forms hydrophobic interactions with the walls of the tunnel, the desosamine sugar projects toward the peptidyl transferase center and interacts with the A2058/A2509 cleft, and the extended alkyl-aryl arm of the drug is oriented down the tunnel and makes contact with a base pair formed by A752 and U2609 of the 23S rRNA. The position of the CEM-101 alkyl-aryl extended arm differs from that reported for the side chain of the ketolide telithromycin complexed with either bacterial (Deinococcus radiodurans) or archaeal (Haloarcula marismortui) large ribosomal subunits but closely matches the position of the side chain of telithromycin complexed to the E. coli ribosome. A difference in the chemical structure of the side chain of CEM-101 in comparison with the side chain of telithromycin and the presence of the fluorine atom at position 2 of the lactone ring likely account for the superior activity of CEM-101. The results of chemical probing suggest that the orientation of the CEM-101 extended side chain observed in the E. coli ribosome closely resembles its placement in Staphylococcus aureus ribosomes and thus likely accurately reflects interaction of CEM-101 with the ribosomes of the pathogenic bacterial targets of the drug. Chemical probing further demonstrated weak binding of CEM-101, but not of erythromycin, to the ribosome dimethylated at A2058 by the action of Erm methyltransferase.


    Organizational Affiliation

    Center for Pharmaceutical Biotechnology-m/c 870, University of Illinois, 900 S. Ashland Ave., Chicago, IL 60607, USA.



Macromolecules

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Entity ID: 3
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50S ribosomal protein L2RCYC271Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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50S ribosomal protein L3RDYD209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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50S ribosomal protein L4REYE201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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50S ribosomal protein L5RFYF178Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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50S ribosomal protein L6RGYG176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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50S ribosomal protein L9RHYH149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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50S ribosomal protein L11RIYI141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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50S ribosomal protein L13RJYJ142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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50S ribosomal protein L14RKYK122Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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50S ribosomal protein L15RLYL143Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L16RMYM136Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L17RNYN120Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L18ROYO116Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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50S ribosomal protein L19RPYP114Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L20RQYQ117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21RRYR103Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L22RSYS110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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50S ribosomal protein L23RTYT93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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50S ribosomal protein L24RUYU102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L25RVYV94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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50S ribosomal protein L27RWYW79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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50S ribosomal protein L28RXYX77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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50S ribosomal protein L29RYYY63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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50S ribosomal protein L30RZYZ58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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50S ribosomal protein L32R0Y056Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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50S ribosomal protein L33R1Y150Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34R2Y246Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L35R3Y364Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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50S ribosomal protein L36R4Y438Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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30S ribosomal protein S2QBXB218Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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30S ribosomal protein S3QCXC206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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30S ribosomal protein S4QDXD205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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30S ribosomal protein S5QEXE150Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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30S ribosomal protein S6QFXF100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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30S ribosomal protein S7QGXG151Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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30S ribosomal protein S8QHXH129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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30S ribosomal protein S9QIXI127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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30S ribosomal protein S10QJXJ98Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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30S ribosomal protein S11QKXK117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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30S ribosomal protein S12QLXL123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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30S ribosomal protein S13QMXM114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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30S ribosomal protein S14QNXN101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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30S ribosomal protein S15QOXO88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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30S ribosomal protein S16QPXP82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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30S ribosomal protein S17QQXQ80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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30S ribosomal protein S18QRXR55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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30S ribosomal protein S19QSXS79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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30S ribosomal protein S20QTXT85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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30S ribosomal protein S21QUXU51Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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23S rRNARA, YA2904Escherichia coli str. K-12 substr. MG1655
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5S rRNARB, YB118Escherichia coli str. K-12 substr. MG1655
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16S rRNAQA, XA1533Escherichia coli str. K-12 substr. MG1655
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EM1
Query on EM1

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RA
(3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside
C43 H65 F N6 O10
IXXFZUPTQVDPPK-ZAWHAJPISA-N
 Ligand Interaction
ZN
Query on ZN

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R4, Y4
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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QA, RA, RB, XA, YA, YB, YE, YJ
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.759α = 90
b = 433.272β = 90
c = 618.863γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release