2OGM

The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.275 

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This is version 1.2 of the entry. See complete history. 


Literature

Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.

Davidovich, C., Bashan, A., Auerbach-Nevo, T., Yaggie, R.D., Gontarek, R.R., Yonath, A.

(2007) Proc Natl Acad Sci U S A 104: 4291-4296

  • DOI: 10.1073/pnas.0700041104
  • Primary Citation of Related Structures:  
    2OGM, 2OGN, 2OGO

  • PubMed Abstract: 

    • New insights into functional flexibility at the peptidyl transferase center (PTC) and its vicinity were obtained by analysis of pleuromutilins binding modes to the ribosome. The crystal structures of Deinococcus radiodurans large ribosomal subunit complexed with each of three pleuromutilin derivatives: retapamulin (SB-275833), SB-280080, and SB-571519, show that all bind to the PTC with their core oriented similarly at the A-site and their C14 extensions pointing toward the P-site ...

    New insights into functional flexibility at the peptidyl transferase center (PTC) and its vicinity were obtained by analysis of pleuromutilins binding modes to the ribosome. The crystal structures of Deinococcus radiodurans large ribosomal subunit complexed with each of three pleuromutilin derivatives: retapamulin (SB-275833), SB-280080, and SB-571519, show that all bind to the PTC with their core oriented similarly at the A-site and their C14 extensions pointing toward the P-site. Except for an H-bond network with a single nucleotide, G2061, which involves the essential keto group of all three compounds, only minor hydrophobic contacts are formed between the pleuromutilin C14 extensions and any ribosomal component, consistent with the PTC tolerance to amino acid diversity. Efficient drug binding mode is attained by a mechanism based on induced-fit motions exploiting the ribosomal intrinsic functional flexibility and resulting in conformational rearrangements that seal the pleuromutilin-binding pocket and tightens it up. Comparative studies identified a network of remote interactions around the PTC, indicating that pleuromutilins selectivity is acquired by nonconserved nucleotides residing in the PTC vicinity, in a fashion resembling allosterism. Likewise, pleuromutilin resistant mechanisms involve nucleotides residing in the environs of the binding pocket, consistent with their slow resistance-development rates.

    Organizational Affiliation: 

    Department of Structural Biology, Weizmann Institute, Rehovot 76100, Israel.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3B211Deinococcus radioduransMutation(s): 0 
UniProt
Find proteins for Q9RXK2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Explore Q9RXK2 
Go to UniProtKB:  Q9RXK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RXK2
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth 0]2,880Deinococcus radiodurans
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G19
Query on G19
Download Ideal Coordinates CCD File 
C [auth 0](2S,3AR,4R,5S,6S,8R,9R,9AR,10R)-2,5-DIHYDROXY-4,6,9,10-TETRAMETHYL-1-OXO-6-VINYLDECAHYDRO-3A,9-PROP[1]ENOCYCLOPENTA[8]ANNULEN-8-YL [(6-AMINOPYRIDAZIN-3-YL)CARBONYL]CARBAMATE
C26 H34 N4 O6
UQIPGFDHSLPFHW-YEAQTOLVSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.275 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.396α = 90
b = 405.835β = 90
c = 703.8γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance