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PDBsum entry 3gu0

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protein links
Chaperone PDB id
3gu0
Jmol
Contents
Protein chain
406 a.a. *
* Residue conservation analysis
PDB id:
3gu0
Name: Chaperone
Title: Promiscuous substrate recognition in folding and assembly ac of the trigger factor chaperone
Structure: Trigger factor. Chain: a. Fragment: residues 1-405. Synonym: tf. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: tig, tm_0694. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
3.50Å     R-factor:   0.250     R-free:   0.358
Authors: E.Martinez-Hackert,W.A.Hendrickson
Key ref:
E.Martinez-Hackert and W.A.Hendrickson (2009). Promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone. Cell, 138, 923-934. PubMed id: 19737520 DOI: 10.1016/j.cell.2009.07.044
Date:
28-Mar-09     Release date:   22-Dec-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9WZF8  (TIG_THEMA) -  Trigger factor
Seq:
Struc:
425 a.a.
406 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!
  Cellular component     cytoplasm   1 term 
  Biological process     cell cycle   5 terms 
  Biochemical function     protein binding     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/j.cell.2009.07.044 Cell 138:923-934 (2009)
PubMed id: 19737520  
 
 
Promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone.
E.Martinez-Hackert, W.A.Hendrickson.
 
  ABSTRACT  
 
Trigger factor (TF) is a molecular chaperone that binds to bacterial ribosomes where it contacts emerging nascent chains, but TF is also abundant free in the cytosol where its activity is less well characterized. In vitro studies show that TF promotes protein refolding. We find here that ribosome-free TF stably associates with and rescues from misfolding a large repertoire of full-length proteins. We identify over 170 members of this cytosolic Escherichia coli TF substrate proteome, including ribosomal protein S7. We analyzed the biochemical properties of a TF:S7 complex from Thermotoga maritima and determined its crystal structure. Thereby, we obtained an atomic-level picture of a promiscuous chaperone in complex with a physiological substrate protein. The structure of the complex reveals the molecular basis of substrate recognition by TF, indicates how TF could accelerate protein folding, and suggests a role for TF in the biogenesis of protein complexes.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Structure of TF in Complex with Ribosomal Protein S7
(A) Ribbon diagram of tmTF colored by domains. The N-terminal domain (NTD) is colored blue; the PPIase domain green; the C-terminal domain (CTD) red. NTD and PPIase are connected via a linker colored yellow here and subsequently colored red as part of CTD. Disordered TF residues shown as a blue dotted line correspond to the ribosome-binding loop. Orientation is a view down the diad axis of the TF:S7 complex.
(B) Ribbon diagram of TF colored by domains as in (A) except for linker, now red. The yellow ribbon corresponds to tmS7 as it is bound inside the CTD cleft. Orientation has the diad axis vertical.
(C) TF:S7 complex. Two TF molecules (ribbons colored by domains as in B encapsulate two S7 molecules (yellow molecular surfaces). Orientation is as rotated 90° from (B) and as in (A) but rotated by vert, similar 30° about the diad axis. Scale is as in (B).
(D) Surface representation of the TF:S7 complex; TF is colored red and blue; S7 is colored yellow.
(E) Ribbon diagram of substrate-free tmTF colored by domains as in (B). The CTD is superimposed onto that of tmTF in the complex as oriented in (B). The yellow ribbon represents a symmetry-related tmTF with its NTD (solid) bound inside the CTD cleft.
(F) Ribbon diagram of substrate-free ecTF colored by domains as in (B). The core of CTD is superimposed onto that of tmTF as oriented in (B) and (E). The yellow ribbon represents a symmetry-related ecTF with its NTD (solid) bound inside the CTD cleft.
Figure 5.
Figure 5. Surface Representations of T. maritima TF and S7
(A) Contact surfaces. The molecular surface of TF (middle) is colored by domains as in 3B but with the imprint of bound S7 colored in yellow. The dark ribbon shows S7. Molecular surfaces of S7 (outside) are rotated to display the imprint of bound TF. Blue residues contact NTD, green contact PPIase, red contact CTD, and magenta contact both NTD and CTD.
(B) Electrostatic potential of TF and S7. Molecular surfaces are oriented as in (A) and S7 is drawn as a yellow ribbon. Surfaces are colored in degrees of positive (blue) and negative (red) potential.
(C) Hydrophobic patches on the tmTF surface. Vicinal apolar atoms that form continuous hydrophobic surfaces are colored blue.
(D) Comparison of the TF:S7 interface with approximately 44,000 structurally defined interfaces between pairs of protein domains cataloged in PYBASE (Davis and Sali, 2005). Properties of the TF:S7 interface are represented by the red and blue spheres (1:1 dimer and 2:2 tetramer, respectively). PYBASE interaction sets are represented by gray spheres. Sc corresponds to shape complementarity value, BSA corresponds to buried surface area, and P/NP corresponds to the ratio of polar versus nonpolar interfacial residues.
 
  The above figures are reprinted by permission from Cell Press: Cell (2009, 138, 923-934) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21059683 O.René, and J.H.Alix (2011).
Late steps of ribosome assembly in E. coli are sensitive to a severe heat stress but are assisted by the HSP70 chaperone machine.
  Nucleic Acids Res, 39, 1855-1867.  
20368618 A.Koplin, S.Preissler, Y.Ilina, M.Koch, A.Scior, M.Erhardt, and E.Deuerling (2010).
A dual function for chaperones SSB-RAC and the NAC nascent polypeptide-associated complex on ribosomes.
  J Cell Biol, 189, 57-68.  
20368615 K.Karbstein (2010).
Chaperoning ribosome assembly.
  J Cell Biol, 189, 11-12.  
20616058 M.D.Daugherty, D.S.Booth, B.Jayaraman, Y.Cheng, and A.D.Frankel (2010).
HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes.
  Proc Natl Acad Sci U S A, 107, 12481-12486.  
19809489 A.Hoffmann, and B.Bukau (2009).
Trigger factor finds new jobs and contacts.
  Nat Struct Mol Biol, 16, 1006-1008.  
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.