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PDBsum entry 2nyo

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protein dna_rna ligands Protein-protein interface(s) links
Structural protein/RNA/antibiotic PDB id
2nyo
Jmol
Contents
Protein chains
134 a.a.
11 a.a.
DNA/RNA
Ligands
XBB-TZO-DHA-PYT
Superseded by: 2jq7 2jq7
PDB id:
2nyo
Name: Structural protein/RNA/antibiotic
Title: Model for thiostrepton binding to the ribosomal l11-RNA region
Structure: 50s ribosomal protein l11. Chain: a. Engineered: yes. Ribosomal RNA. Chain: b. Fragment: l11 binding domain, residues 1051-1108. Engineered: yes. Thiostrepton antibiotic. Chain: c
Source: Thermotoga maritima. Gene: rplk. Expressed in: escherichia coli. Synthetic: yes. Other_details: in vitro transcribed RNA construct based on sequence naturally found in escherichia coli.. Streptomyces azureus. Bacteria. Other_details: purchased from sigma.
NMR struc: 10 models
Authors: H.R.A.Jonker,S.Ilin,S.K.Grimm,J.Woehnert,H.Schwalbe
Key ref: H.R.Jonker et al. (2007). L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy. Nucleic Acids Res, 35, 441-454. PubMed id: 17169991
Date:
21-Nov-06     Release date:   06-Feb-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29395  (RL11_THEMA) -  50S ribosomal protein L11
Seq:
Struc:
141 a.a.
134 a.a.
Protein chain
No UniProt id for this chain
Struc: 11 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Nucleic Acids Res 35:441-454 (2007)
PubMed id: 17169991  
 
 
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
H.R.Jonker, S.Ilin, S.K.Grimm, J.Wöhnert, H.Schwalbe.
 
  ABSTRACT  
 
Ribosomal proteins are assumed to stabilize specific RNA structures and promote compact folding of the large rRNA. The conformational dynamics of the protein between the bound and unbound state play an important role in the binding process. We have studied those dynamical changes in detail for the highly conserved complex between the ribosomal protein L11 and the GTPase region of 23S rRNA. The RNA domain is compactly folded into a well defined tertiary structure, which is further stabilized by the association with the C-terminal domain of the L11 protein (L11(ctd)). In addition, the N-terminal domain of L11 (L11(ntd)) is implicated in the binding of the natural thiazole antibiotic thiostrepton, which disrupts the elongation factor function. We have studied the conformation of the ribosomal protein and its dynamics by NMR in the unbound state, the RNA bound state and in the ternary complex with the RNA and thiostrepton. Our data reveal a rearrangement of the L11(ntd), placing it closer to the RNA after binding of thiostrepton, which may prevent binding of elongation factors. We propose a model for the ternary L11-RNA-thiostrepton complex that is additionally based on interaction data and conformational information of the L11 protein. The model is consistent with earlier findings and provides an explanation for the role of L11(ntd) in elongation factor binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22407015 L.Wang, F.Yang, D.Zhang, Z.Chen, R.M.Xu, K.H.Nierhaus, W.Gong, and Y.Qin (2012).
A conserved proline switch on the ribosome facilitates the recruitment and binding of trGTPases.
  Nat Struct Mol Biol, 19, 403-410.  
21241883 C.Dominguez, M.Schubert, O.Duss, S.Ravindranathan, and F.H.Allain (2011).
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy.
  Prog Nucl Magn Reson Spectrosc, 58, 1.  
19875082 A.L.Starosta, H.Qin, A.Mikolajka, G.Y.Leung, K.Schwinghammer, K.C.Nicolaou, D.Y.Chen, B.S.Cooperman, and D.N.Wilson (2009).
Identification of distinct thiopeptide-antibiotic precursor lead compounds using translation machinery assays.
  Chem Biol, 16, 1087-1096.  
19921000 S.Schoof, and H.D.Arndt (2009).
D-cysteine occurrence in thiostrepton may not necessitate an epimerase.
  Chem Commun (Camb), (), 7113-7115.  
18611379 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2008).
Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase.
  Structure, 16, 1059-1066.
PDB codes: 3cjq 3cjr 3cjs 3cjt 3cju 3egv
18084030 H.J.Haiser, F.V.Karginov, G.J.Hannon, and M.A.Elliot (2008).
Developmentally regulated cleavage of tRNAs in the bacterium Streptomyces coelicolor.
  Nucleic Acids Res, 36, 732-741.  
18406324 J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.Spahn, and P.Fucini (2008).
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
  Mol Cell, 30, 26-38.
PDB codes: 2zjp 2zjq 2zjr 3cf5
18957331 K.B.Hall (2008).
RNA in motion.
  Curr Opin Chem Biol, 12, 612-618.  
17940088 A.García-Marcos, A.Morreale, E.Guarinos, E.Briones, M.Remacha, A.R.Ortiz, and J.P.Ballesta (2007).
In vivo assembling of bacterial ribosomal protein L11 into yeast ribosomes makes the particles sensitive to the prokaryotic specific antibiotic thiostrepton.
  Nucleic Acids Res, 35, 7109-7117.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.