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PDBsum entry 1aci

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protein links
Ribosomal protein PDB id
1aci
Jmol
Contents
Protein chain
76 a.a. *
* Residue conservation analysis
PDB id:
1aci
Name: Ribosomal protein
Title: L11 ribosomal protein RNA binding domain, nmr, 20 structures
Structure: L11 ribosomal protein. Chain: a. Fragment: c-terminal domain, 76 residues
Source: Geobacillus stearothermophilus. Organism_taxid: 1422. Strain: l11
NMR struc: 20 models
Authors: Y.Xing,D.E.Draper
Key ref:
Y.Xing and D.E.Draper (1996). Cooperative interactions of RNA and thiostrepton antibiotic with two domains of ribosomal protein L11. Biochemistry, 35, 1581-1588. PubMed id: 8634289 DOI: 10.1021/bi952132o
Date:
07-Feb-97     Release date:   14-Jan-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P56210  (RL11_GEOSE) -  50S ribosomal protein L11 (Fragment)
Seq:
Struc:
133 a.a.
76 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ribosome   1 term 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     1 term  

 

 
DOI no: 10.1021/bi952132o Biochemistry 35:1581-1588 (1996)
PubMed id: 8634289  
 
 
Cooperative interactions of RNA and thiostrepton antibiotic with two domains of ribosomal protein L11.
Y.Xing, D.E.Draper.
 
  ABSTRACT  
 
Ribosomal protein L11 interacts with a 58-nucleotide domain of large subunit ribosomal RNA; both the protein and its RNA target have been highly conserved. The antibiotic thiostrepton recognizes the same RNA domain, and binds to the ribosome cooperatively with L11. Experiments presented here show that RNA recognition and thiostrepton cooperativity can be attributed to C- and N-terminal domains of L11, respectively. Under trypsin digestion conditions that degrade Bacillus stearothermophilus L11 to small fragments, the target RNA protects the C-terminal 77 residues from digestion, and thiostrepton and RNA in combination protect the entire protein. A 76-residue C-terminal fragment of L11 was overexpressed and shown to fold into a stable structure binding ribosomal RNA with essentially the same properties as full-length L11. An L11.thiostrepton.RNA complex was 100-200-fold more stable than expected on the basis of L11-RNA and thiostrepton-RNA binding affinities; similar measurements with the C-terminal fragment detected no cooperativity with thiostrepton. L11 function is thus more complex than simple interaction with ribosomal RNA; we suggest that thiostrepton mimics some ribosomal component or factor that normally interacts with the L11 N-terminal domain.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20179875 M.A.Ciufolini, and D.Lefranc (2010).
Micrococcin P1: structure, biology and synthesis.
  Nat Prod Rep, 27, 330-342.  
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.  
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
  19130444 K.C.Nicolaou, J.S.Chen, D.J.Edmonds, and A.A.Estrada (2009).
Recent advances in the chemistry and biology of naturally occurring antibiotics.
  Angew Chem Int Ed Engl, 48, 660-719.  
19072817 S.Schoof, S.Baumann, B.Ellinger, and H.D.Arndt (2009).
A Fluorescent Probe for the 70 S-Ribosomal GTPase-Associated Center.
  Chembiochem, 10, 242-245.  
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
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.  
17169991 H.R.Jonker, S.Ilin, S.K.Grimm, J.Wöhnert, and H.Schwalbe (2007).
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
  Nucleic Acids Res, 35, 441-454.
PDB codes: 2jq7 2nyo
16716074 C.Maeder, G.L.Conn, and D.E.Draper (2006).
Optimization of a ribosomal structural domain by natural selection.
  Biochemistry, 45, 6635-6643.  
16556224 H.Sato, K.Ito, and Y.Nakamura (2006).
Ribosomal protein L11 mutations in two functional domains equally affect release factors 1 and 2 activity.
  Mol Microbiol, 60, 108-120.  
16094695 S.Ilin, A.Hoskins, O.Ohlenschläger, H.R.Jonker, H.Schwalbe, and J.Wöhnert (2005).
Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima.
  Chembiochem, 6, 1611-1618.
PDB code: 2k3f
15972821 S.L.Bausch, E.Poliakova, and D.E.Draper (2005).
Interactions of the N-terminal domain of ribosomal protein L11 with thiostrepton and rRNA.
  J Biol Chem, 280, 29956-29963.  
15919197 T.Hermann (2005).
Drugs targeting the ribosome.
  Curr Opin Struct Biol, 15, 355-366.  
15492007 W.S.Bowen, N.Van Dyke, E.J.Murgola, J.S.Lodmell, and W.E.Hill (2005).
Interaction of thiostrepton and elongation factor-G with the ribosomal protein L11-binding domain.
  J Biol Chem, 280, 2934-2943.  
14977044 D.Triantafillidou, E.Persidou, D.Lazarou, P.Andrikopoulos, F.Leontiadou, and T.Choli-Papadopoulou (2004).
Structural destabilization of the recombinant thermophilic TthL11 ribosomal protein by a single amino acid substitution.
  Biol Chem, 385, 31-39.  
12925990 T.Hermann (2003).
Chemical and functional diversity of small molecule ligands for RNA.
  Biopolymers, 70, 4.  
12198134 T.Uchiumi, S.Honma, Y.Endo, and A.Hachimori (2002).
Ribosomal proteins at the stalk region modulate functional rRNA structures in the GTPase center.
  J Biol Chem, 277, 41401-41409.  
11807083 W.Xu, F.T.Pagel, and E.J.Murgola (2002).
Mutations in the GTPase center of Escherichia coli 23S rRNA indicate release factor 2-interactive sites.
  J Bacteriol, 184, 1200-1203.  
11504736 P.J.Schlax, K.A.Xavier, T.C.Gluick, and D.E.Draper (2001).
Translational repression of the Escherichia coli alpha operon mRNA: importance of an mRNA conformational switch and a ternary entrapment complex.
  J Biol Chem, 276, 38494-38501.  
11673421 X.Yang, and E.E.Ishiguro (2001).
Involvement of the N terminus of ribosomal protein L11 in regulation of the RelA protein of Escherichia coli.
  J Bacteriol, 183, 6532-6537.  
11018283 A.L.Arkov, D.V.Freistroffer, M.Y.Pavlov, M.Ehrenberg, and E.J.Murgola (2000).
Mutations in conserved regions of ribosomal RNAs decrease the productive association of peptide-chain release factors with the ribosome during translation termination.
  Biochimie, 82, 671-682.  
10675344 B.L.Staker, P.Korber, J.C.Bardwell, and M.A.Saper (2000).
Structure of Hsp15 reveals a novel RNA-binding motif.
  EMBO J, 19, 749-757.
PDB code: 1dm9
10799526 D.I.Svergun, and K.H.Nierhaus (2000).
A map of protein-rRNA distribution in the 70 S Escherichia coli ribosome.
  J Biol Chem, 275, 14432-14439.  
10734197 L.B.Blyn, L.M.Risen, R.H.Griffey, and D.E.Draper (2000).
The RNA-binding domain of ribosomal protein L11 recognizes an rRNA tertiary structure stabilized by both thiostrepton and magnesium ion.
  Nucleic Acids Res, 28, 1778-1784.  
10338213 B.T.Wimberly, R.Guymon, J.P.McCutcheon, S.W.White, and V.Ramakrishnan (1999).
A detailed view of a ribosomal active site: the structure of the L11-RNA complex.
  Cell, 97, 491-502.
PDB code: 1mms
10090750 D.GuhaThakurta, and D.E.Draper (1999).
Protein-RNA sequence covariation in a ribosomal protein-rRNA complex.
  Biochemistry, 38, 3633-3640.  
10325228 G.L.Conn, D.E.Draper, E.E.Lattman, and A.G.Gittis (1999).
Crystal structure of a conserved ribosomal protein-RNA complex.
  Science, 284, 1171-1174.
PDB code: 1qa6
10400688 M.L.Chiu, M.Folcher, T.Katoh, A.M.Puglia, J.Vohradsky, B.S.Yun, H.Seto, and C.J.Thompson (1999).
Broad spectrum thiopeptide recognition specificity of the Streptomyces lividans TipAL protein and its role in regulating gene expression.
  J Biol Chem, 274, 20578-20586.  
10488095 T.Uchiumi, K.Hori, T.Nomura, and A.Hachimori (1999).
Replacement of L7/L12.L10 protein complex in Escherichia coli ribosomes with the eukaryotic counterpart changes the specificity of elongation factor binding.
  J Biol Chem, 274, 27578-27582.  
9718323 G.L.Conn, R.R.Gutell, and D.E.Draper (1998).
A functional ribosomal RNA tertiary structure involves a base triple interaction.
  Biochemistry, 37, 11980-11988.  
9666324 S.A.Woodson, and N.B.Leontis (1998).
Structure and dynamics of ribosomal RNA.
  Curr Opin Struct Biol, 8, 294-300.  
8989311 A.Yonath, and F.Franceschi (1997).
New RNA recognition features revealed in ancient ribosomal proteins.
  Nat Struct Biol, 4, 3-5.  
8989327 M.A.Markus, A.P.Hinck, S.Huang, D.E.Draper, and D.A.Torchia (1997).
High resolution solution structure of ribosomal protein L11-C76, a helical protein with a flexible loop that becomes structured upon binding to RNA.
  Nat Struct Biol, 4, 70-77.
PDB codes: 1fow 1fox
9013569 T.Uchiumi, and R.Kominami (1997).
Binding of mammalian ribosomal protein complex P0.P1.P2 and protein L12 to the GTPase-associated domain of 28 S ribosomal RNA and effect on the accessibility to anti-28 S RNA autoantibody.
  J Biol Chem, 272, 3302-3308.  
8989317 Y.Xing, D.Guha Thakurta, and D.E.Draper (1997).
The RNA binding domain of ribosomal protein L11 is structurally similar to homeodomains.
  Nat Struct Biol, 4, 24-27.  
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.