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PDBsum entry 2gw1

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protein Protein-protein interface(s) links
Protein transport PDB id
2gw1
Jmol
Contents
Protein chains
487 a.a. *
Waters ×126
* Residue conservation analysis
PDB id:
2gw1
Name: Protein transport
Title: Crystal structure of the yeast tom70
Structure: Mitochondrial precursor proteins import receptor. Chain: a, b. Fragment: cytosolic fragment. Synonym: 70 kda mitochondrial outer membrane protein, translocase of outer membrane tom70. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: tom70, mas70, omp1. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
3.00Å     R-factor:   0.259     R-free:   0.316
Authors: Y.Wu,B.Sha
Key ref:
Y.Wu and B.Sha (2006). Crystal structure of yeast mitochondrial outer membrane translocon member Tom70p. Nat Struct Mol Biol, 13, 589-593. PubMed id: 16767096 DOI: 10.1038/nsmb1106
Date:
03-May-06     Release date:   27-Jun-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P07213  (TOM70_YEAST) -  Mitochondrial import receptor subunit TOM70
Seq:
Struc:
 
Seq:
Struc:
617 a.a.
487 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrial outer membrane   1 term 
  Biological process     intracellular protein transport   1 term 
  Biochemical function     P-P-bond-hydrolysis-driven protein transmembrane transporter activity     1 term  

 

 
DOI no: 10.1038/nsmb1106 Nat Struct Mol Biol 13:589-593 (2006)
PubMed id: 16767096  
 
 
Crystal structure of yeast mitochondrial outer membrane translocon member Tom70p.
Y.Wu, B.Sha.
 
  ABSTRACT  
 
A majority of the proteins targeted to the mitochondria are transported through the translocase of the outer membrane (TOM) complex. Tom70 is a major surface receptor for mitochondrial protein precursors in the TOM complex. To investigate how Tom70 receives the mitochondrial protein precursors, we have determined the crystal structure of yeast Tom70p to 3.0 A. Tom70p forms a homodimer in the crystal. Each subunit consists primarily of tetratricopeptide repeat (TPR) motifs, which are organized into a right-handed superhelix. The TPR motifs in the N-terminal domain of Tom70p form a peptide-binding groove for the C-terminal EEVD motif of Hsp70, whereas the C-terminal domain of Tom70p contains a large pocket that may be the binding site for mitochondrial precursors. The crystal structure of Tom70p provides insights into the mechanisms of precursor transport across the mitochondrion's outer membrane.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Tom70p monomer structure, shown as ribbons in stereo view^31. N- and C-terminal domains are shown in blue and green, respectively, and TPR motifs are labeled. Oval marks the disordered region between the domains.
Figure 4.
Figure 4. The putative mitochondrial preprotein–binding pocket of Tom70p. The sequence-conservation score obtained by the sequence alignment from Figure 3 was mapped to the Tom70p molecular surface by GRASP. Green and pink denote conserved and unconserved regions, respectively. (a) Sequence-conservation drawing for the Tom70p monomer. Orientation of Tom70p in the left panel is similar to that of left monomer in Figure 2a. Red box marks putative preprotein-binding pocket, and Tom70p dimer interface is labeled. Right panel shows a view rotated 180° along the vertical axis from that in the left panel, with binding site for Hsp70 C terminus labeled. (b) Enlarged view of the preprotein-binding pocket region shown in red box in a. Oval marks disordered linker region between the Tom70p N- and C-terminal domains. Conserved residues located in the opening (Arg443 and Asp477) and lower half of the pocket (Glu473, Glu542 and Glu577) are labeled. (c) Sequence-conservation drawing for the upper half of the Tom70p preprotein-binding pocket inner surface. This figure was generated by viewing the inner surface of the pocket vertically from bottom to top when Tom70p is oriented as in b. Conserved residues forming the upper half of the inner surface are labeled in white, and the two conserved residues at the opening of the pocket (Arg443 and Asp477) are labeled in yellow.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 589-593) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20871025 A.D.Tsaousis, D.Gaston, A.Stechmann, P.B.Walker, T.Lithgow, and A.J.Roger (2011).
A functional Tom70 in the human parasite Blastocystis sp.: implications for the evolution of the mitochondrial import apparatus.
  Mol Biol Evol, 28, 781-791.  
21139638 E.Schleiff, and T.Becker (2011).
Common ground for protein translocation: access control for mitochondria and chloroplasts.
  Nat Rev Mol Cell Biol, 12, 48-59.  
20504278 A.C.Fan, L.M.Gava, C.H.Ramos, and J.C.Young (2010).
Human mitochondrial import receptor Tom70 functions as a monomer.
  Biochem J, 429, 553-563.  
20184891 J.Tao, K.Petrova, D.Ron, and B.Sha (2010).
Crystal structure of P58(IPK) TPR fragment reveals the mechanism for its molecular chaperone activity in UPR.
  J Mol Biol, 397, 1307-1315.
PDB code: 3ieg
20628368 X.Y.Liu, B.Wei, H.X.Shi, Y.F.Shan, and C.Wang (2010).
Tom70 mediates activation of interferon regulatory factor 3 on mitochondria.
  Cell Res, 20, 994.  
19703392 A.Chacinska, C.M.Koehler, D.Milenkovic, T.Lithgow, and N.Pfanner (2009).
Importing mitochondrial proteins: machineries and mechanisms.
  Cell, 138, 628-644.  
19091741 D.Han, K.Kim, Y.Kim, Y.Kang, J.Y.Lee, and Y.Kim (2009).
Crystal structure of the N-terminal domain of anaphase-promoting complex subunit 7.
  J Biol Chem, 284, 15137-15146.
PDB code: 3ffl
19767391 H.Yamamoto, K.Fukui, H.Takahashi, S.Kitamura, T.Shiota, K.Terao, M.Uchida, M.Esaki, S.Nishikawa, T.Yoshihisa, K.Yamano, and T.Endo (2009).
Roles of Tom70 in import of presequence-containing mitochondrial proteins.
  J Biol Chem, 284, 31635-31646.  
19581297 J.Li, X.Qian, J.Hu, and B.Sha (2009).
Molecular chaperone Hsp70/Hsp90 prepares the mitochondrial outer membrane translocon receptor Tom71 for preprotein loading.
  J Biol Chem, 284, 23852-23859.
PDB codes: 3fp2 3fp3 3fp4
19028997 R.F.Waller, C.Jabbour, N.C.Chan, N.Celik, V.A.Likic, T.D.Mulhern, and T.Lithgow (2009).
Evidence of a reduced and modified mitochondrial protein import apparatus in microsporidian mitosomes.
  Eukaryot Cell, 8, 19-26.  
19453276 T.Endo, and K.Yamano (2009).
Multiple pathways for mitochondrial protein traffic.
  Biol Chem, 390, 723-730.  
19182809 T.J.Knowles, A.Scott-Tucker, M.Overduin, and I.R.Henderson (2009).
Membrane protein architects: the role of the BAM complex in outer membrane protein assembly.
  Nat Rev Microbiol, 7, 206-214.  
17634984 M.Palaiomylitou, A.Tartas, D.Vlachakis, D.Tzamarias, and M.Vlassi (2008).
Investigating the structural stability of the Tup1-interaction domain of Ssn6: evidence for a conformational change on the complex.
  Proteins, 70, 72-82.  
18007655 N.Kondo-Okamoto, J.M.Shaw, and K.Okamoto (2008).
Tetratricopeptide repeat proteins Tom70 and Tom71 mediate yeast mitochondrial morphogenesis.
  EMBO Rep, 9, 63-69.  
18759741 X.Gatsos, A.J.Perry, K.Anwari, P.Dolezal, P.P.Wolynec, V.A.Likić, A.W.Purcell, S.K.Buchanan, and T.Lithgow (2008).
Protein secretion and outer membrane assembly in Alphaproteobacteria.
  FEMS Microbiol Rev, 32, 995.  
18359807 Y.Itoh, J.D.Rice, C.Goller, A.Pannuri, J.Taylor, J.Meisner, T.J.Beveridge, J.F.Preston, and T.Romeo (2008).
Roles of pgaABCD genes in synthesis, modification, and export of the Escherichia coli biofilm adhesin poly-beta-1,6-N-acetyl-D-glucosamine.
  J Bacteriol, 190, 3670-3680.  
17825565 M.J.Baker, A.E.Frazier, J.M.Gulbis, and M.T.Ryan (2007).
Mitochondrial protein-import machinery: correlating structure with function.
  Trends Cell Biol, 17, 456-464.  
17596514 M.K.Bhangoo, S.Tzankov, A.C.Fan, K.Dejgaard, D.Y.Thomas, and J.C.Young (2007).
Multiple 40-kDa heat-shock protein chaperones function in Tom70-dependent mitochondrial import.
  Mol Biol Cell, 18, 3414-3428.  
17263664 W.Neupert, and J.M.Herrmann (2007).
Translocation of proteins into mitochondria.
  Annu Rev Biochem, 76, 723-749.  
16822835 C.H.Chou, R.S.Lee, and H.F.Yang-Yen (2006).
An internal EELD domain facilitates mitochondrial targeting of Mcl-1 via a Tom70-dependent pathway.
  Mol Biol Cell, 17, 3952-3963.  
17099692 R.Albrecht, P.Rehling, A.Chacinska, J.Brix, S.A.Cadamuro, R.Volkmer, B.Guiard, N.Pfanner, and K.Zeth (2006).
The Tim21 binding domain connects the preprotein translocases of both mitochondrial membranes.
  EMBO Rep, 7, 1233-1238.
PDB code: 2ciu
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 code is shown on the right.