spacer
spacer

PDBsum entry 1p9y

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Isomerase PDB id
1p9y
Jmol
Contents
Protein chains
117 a.a. *
Ligands
ACY ×3
Waters ×209
* Residue conservation analysis
PDB id:
1p9y
Name: Isomerase
Title: Ribosome binding of e. Coli trigger factor mutant f44l.
Structure: Trigger factor. Chain: a, b. Fragment: ribosome binding domain. Synonym: tf. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: tig. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.15Å     R-factor:   0.200     R-free:   0.247
Authors: O.Kristensen,M.Gajhede
Key ref:
O.Kristensen and M.Gajhede (2003). Chaperone binding at the ribosomal exit tunnel. Structure, 11, 1547-1556. PubMed id: 14656439 DOI: 10.1016/j.str.2003.11.003
Date:
13-May-03     Release date:   16-Dec-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A850  (TIG_ECOLI) -  Trigger factor
Seq:
Struc:
432 a.a.
117 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.5.2.1.8  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein transport   2 terms 

 

 
    Added reference    
 
 
DOI no: 10.1016/j.str.2003.11.003 Structure 11:1547-1556 (2003)
PubMed id: 14656439  
 
 
Chaperone binding at the ribosomal exit tunnel.
O.Kristensen, M.Gajhede.
 
  ABSTRACT  
 
The exit tunnel region of the ribosome is well established as a focal point for interaction between the components that guide the fate of nascent polypeptides. One of these, the chaperone trigger factor (TF), associates with the 50S ribosomal subunit through its N-terminal domain. Targeting of TF to ribosomes is crucial to achieve its remarkable efficiency in protein folding. A similar tight coupling to translation is found in signal recognition particle (SRP)-dependent protein translocation. Here, we report crystal structures of the E. coli TF ribosome binding domain. TF is structurally related to the Hsp33 chaperone but has a prominent ribosome anchor located as a tip of the molecule. This tip includes the previously established unique TF signature motif. Comparison reveals that this feature is not found in SRP structures. We identify a conserved helical kink as a hallmark of the TF structure that is most likely critical to ensure ribosome association.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Hallmarks of the TFrb Structure(A) Electrostatic properties of the TFrb structure displayed as a GRASP (Honig and Nicholls, 1995) surface. A region containing many basic residues is located at the tip of the molecule while negative charges dominate one face of the b sheet of the structural core.(B) Stereo view of the ribosomal anchor region, molecule B.(C) We observe different loop conformations of the ribosomal anchor. From left to right (blue to light green) are shown the three conformers observed in the SeMet-TFrb crystal. The conformation of the loop in the F44L structure (yellow) is most similar to the least well-defined loop configuration, molecule C.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1547-1556) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18043871 Y.Yao, G.Bhabha, G.Kroon, M.Landes, and H.J.Dyson (2008).
Structure discrimination for the C-terminal domain of Escherichia coli trigger factor in solution.
  J Biomol NMR, 40, 23-30.  
17372359 E.Martinez-Hackert, and W.A.Hendrickson (2007).
Structures of and interactions between domains of trigger factor from Thermotoga maritima.
  Acta Crystallogr D Biol Crystallogr, 63, 536-547.
PDB codes: 2nsa 2nsb 2nsc
17296610 S.K.Lakshmipathy, S.Tomic, C.M.Kaiser, H.C.Chang, P.Genevaux, C.Georgopoulos, J.M.Barral, A.E.Johnson, F.U.Hartl, and S.A.Etchells (2007).
Identification of nascent chain interaction sites on trigger factor.
  J Biol Chem, 282, 12186-12193.  
16271892 F.Schlünzen, D.N.Wilson, P.Tian, J.M.Harms, S.J.McInnes, H.A.Hansen, R.Albrecht, J.Buerger, S.M.Wilbanks, and P.Fucini (2005).
The binding mode of the trigger factor on the ribosome: implications for protein folding and SRP interaction.
  Structure, 13, 1685-1694.
PDB code: 2d3o
15334087 L.Ferbitz, T.Maier, H.Patzelt, B.Bukau, E.Deuerling, and N.Ban (2004).
Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins.
  Nature, 431, 590-596.
PDB codes: 1w26 1w2b
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.