spacer
spacer

PDBsum entry 2k3f

Go to PDB code: 
protein links
Ribosomal protein PDB id
2k3f
Jmol
Contents
Protein chain
141 a.a. *
* Residue conservation analysis
PDB id:
2k3f
Name: Ribosomal protein
Title: Ribosomal protein l11 from thermotoga maritima
Structure: 50s ribosomal protein l11. Chain: a. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: rplk. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: H.R.A.Jonker,S.Ilin,H.Schwalbe,J.Woehnert
Key ref: S.Ilin et al. (2005). Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima. Chembiochem, 6, 1611-1618. PubMed id: 16094695
Date:
06-May-08     Release date:   17-Jun-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29395  (RL11_THEMA) -  50S ribosomal protein L11
Seq:
Struc:
141 a.a.
141 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ribonucleoprotein complex   2 terms 
  Biological process     translation   1 term 
  Biochemical function     structural constituent of ribosome     4 terms  

 

 
Chembiochem 6:1611-1618 (2005)
PubMed id: 16094695  
 
 
Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima.
S.Ilin, A.Hoskins, O.Ohlenschläger, H.R.Jonker, H.Schwalbe, J.Wöhnert.
 
  ABSTRACT  
 
L11, a protein of the large ribosomal subunit, binds to a highly conserved domain of 23S rRNA and mediates ribosomal GTPase activity. Its C-terminal domain is the main determinant for rRNA binding, whereas its N-terminal domain plays only a limited role in RNA binding. The N-terminal domain is thought to be involved in interactions with elongation and release factors as well as with the antibiotics thiostrepton and micrococcin. This report presents the NMR solution structure of the full-length L11 protein from the thermophilic eubacterium Thermotoga maritima in its free form. The structure is based on a large number of orientational restraints derived from residual dipolar couplings in addition to conventional NOE-based restraints. The solution structure of L11 demonstrates that, in contrast to many other multidomain RNA-binding proteins, the relative orientation of the two domains is well defined. This is shown both by heteronuclear 15N-relaxation and residual dipolar-coupling data. Comparison of this NMR structure with the X-ray structure of RNA-bound L11, reveals that binding not only induces a rigidification of a flexible loop in the C-terminal domain, but also a sizeable reorientation of the N-terminal domain. The domain orientation in free L11 shows limited similarity to that of ribosome-bound L11 in complex with elongation factor, EF-G.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18957331 K.B.Hall (2008).
RNA in motion.
  Curr Opin Chem Biol, 12, 612-618.  
18004759 S.O.Yesylevskyy, V.N.Kharkyanen, and A.P.Demchenko (2008).
The blind search for the closed states of hinge-bending proteins.
  Proteins, 71, 831-843.  
17610498 B.Polevoda, and F.Sherman (2007).
Methylation of proteins involved in translation.
  Mol Microbiol, 65, 590-606.  
17292917 D.Lee, J.D.Walsh, P.Yu, M.A.Markus, T.Choli-Papadopoulou, C.D.Schwieters, S.Krueger, D.E.Draper, and Y.X.Wang (2007).
The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.
  J Mol Biol, 367, 1007-1022.
PDB codes: 2e34 2e35 2e36 2h8w
17215866 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2007).
Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA.
  EMBO J, 26, 567-577.
PDB codes: 2nxc 2nxe 2nxj 2nxn
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
17064285 S.B.Conners, E.F.Mongodin, M.R.Johnson, C.I.Montero, K.E.Nelson, and R.M.Kelly (2006).
Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species.
  FEMS Microbiol Rev, 30, 872-905.  
16877502 S.O.Yesylevskyy, V.N.Kharkyanen, and A.P.Demchenko (2006).
The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon?
  Biophys J, 91, 3002-3013.  
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.