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PDBsum entry 2v1s

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2v1s
Jmol
Contents
Protein chains
66 a.a. *
69 a.a. *
71 a.a. *
14 a.a. *
12 a.a. *
11 a.a. *
13 a.a. *
Ligands
LEU-LEU-SER-TYR-
ALA-GLY-CY3
ARG-LEU-SER-ARG-
LEU-LEU-SER-TYR-
ALA
Waters ×377
* Residue conservation analysis
PDB id:
2v1s
Name: Oxidoreductase
Title: Crystal structure of rat tom20-aldh presequence complex
Structure: Mitochondrial import receptor subunit tom20 homol chain: a, b, c, d, e, f, g. Fragment: cytosolic domain, residues 59-126. Synonym: mitochondrial 20 kda outer membrane protein, outer mitochondrial membrane receptor tom20. Engineered: yes. Aldehyde dehydrogenase. Chain: h, i, j, k, l, m, n. Fragment: c-terminal half of the presequence, residues 12-2
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Organism_taxid: 10116
Resolution:
2.05Å     R-factor:   0.254     R-free:   0.308
Authors: T.Obita,M.Igura,T.Ose,T.Endo,K.Maenaka,D.Kohda
Key ref: T.Saitoh et al. (2007). Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states. EMBO J, 26, 4777-4787. PubMed id: 17948058
Date:
29-May-07     Release date:   12-Jun-07    
Supersedes: 2cuv
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q62760  (TOM20_RAT) -  Mitochondrial import receptor subunit TOM20 homolog
Seq:
Struc:
145 a.a.
66 a.a.
Protein chains
Pfam   ArchSchema ?
Q62760  (TOM20_RAT) -  Mitochondrial import receptor subunit TOM20 homolog
Seq:
Struc:
145 a.a.
69 a.a.*
Protein chain
Pfam   ArchSchema ?
Q62760  (TOM20_RAT) -  Mitochondrial import receptor subunit TOM20 homolog
Seq:
Struc:
145 a.a.
71 a.a.*
Protein chain
Pfam   ArchSchema ?
Q62760  (TOM20_RAT) -  Mitochondrial import receptor subunit TOM20 homolog
Seq:
Struc:
145 a.a.
14 a.a.
Protein chain
Pfam   ArchSchema ?
P11884  (ALDH2_RAT) -  Aldehyde dehydrogenase, mitochondrial
Seq:
Struc:
519 a.a.
12 a.a.*
Protein chains
Pfam   ArchSchema ?
P11884  (ALDH2_RAT) -  Aldehyde dehydrogenase, mitochondrial
Seq:
Struc:
519 a.a.
11 a.a.*
Protein chains
No UniProt id for this chain
Struc: 13 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 10 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains H, I, K, L: E.C.1.2.1.3  - Aldehyde dehydrogenase (NAD(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An aldehyde + NAD+ + H2O = a carboxylate + NADH
aldehyde
Bound ligand (Het Group name = GLY)
matches with 40.00% similarity
+ NAD(+)
+ H(2)O
= carboxylate
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrial outer membrane translocase complex   1 term 
  Biological process     intracellular protein transport   2 terms 

 

 
    reference    
 
 
EMBO J 26:4777-4787 (2007)
PubMed id: 17948058  
 
 
Tom20 recognizes mitochondrial presequences through dynamic equilibrium among multiple bound states.
T.Saitoh, M.Igura, T.Obita, T.Ose, R.Kojima, K.Maenaka, T.Endo, D.Kohda.
 
  ABSTRACT  
 
Most mitochondrial proteins are synthesized in the cytosol and imported into mitochondria. The N-terminal presequences of mitochondrial-precursor proteins contain a diverse consensus motif (phi chi chi phi phi, phi is hydrophobic and chi is any amino acid), which is recognized by the Tom20 protein on the mitochondrial surface. To reveal the structural basis of the broad selectivity of Tom20, the Tom20-presequence complex was crystallized. Tethering a presequence peptide to Tom20 through a disulfide bond was essential for crystallization. Unexpectedly, the two crystals with different linker designs provided unique relative orientations of the presequence with respect to Tom20, and neither configuration could fully account for the hydrophobic preference at the three hydrophobic positions of the consensus motif. We propose the existence of a dynamic equilibrium in solution among multiple states including the two bound states. In accordance, NMR 15N relaxation analyses suggested motion on a sub-millisecond timescale at the Tom20-presequence interface. We suggest that the dynamic, multiple-mode interaction is the molecular mechanism facilitating the broadly selective specificity of the Tom20 receptor toward diverse mitochondrial presequences.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
21173275 H.Yamamoto, N.Itoh, S.Kawano, Y.Yatsukawa, T.Momose, T.Makio, M.Matsunaga, M.Yokota, M.Esaki, T.Shodai, D.Kohda, A.E.Hobbs, R.E.Jensen, and T.Endo (2011).
Dual role of the receptor Tom20 in specificity and efficiency of protein import into mitochondria.
  Proc Natl Acad Sci U S A, 108, 91-96.  
20729931 O.Schmidt, N.Pfanner, and C.Meisinger (2010).
Mitochondrial protein import: from proteomics to functional mechanisms.
  Nat Rev Mol Cell Biol, 11, 655-667.  
  20925597 S.Baratchi, R.K.Kanwar, and J.R.Kanwar (2010).
Survivin: a target from brain cancer to neurodegenerative disease.
  Crit Rev Biochem Mol Biol, 45, 535-554.  
20124346 T.Lithgow, and A.Schneider (2010).
Evolution of macromolecular import pathways in mitochondria, hydrogenosomes and mitosomes.
  Philos Trans R Soc Lond B Biol Sci, 365, 799-817.  
21102411 Y.Sato, H.Shibata, T.Nakatsu, H.Nakano, Y.Kashiwayama, T.Imanaka, and H.Kato (2010).
Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p.
  EMBO J, 29, 4083-4093.
PDB code: 3ajb
19703392 A.Chacinska, C.M.Koehler, D.Milenkovic, T.Lithgow, and N.Pfanner (2009).
Importing mitochondrial proteins: machineries and mechanisms.
  Cell, 138, 628-644.  
19187233 C.Carrie, E.Giraud, and J.Whelan (2009).
Protein transport in organelles: Dual targeting of proteins to mitochondria and chloroplasts.
  FEBS J, 276, 1187-1195.  
19841628 D.D.Boehr, R.Nussinov, and P.E.Wright (2009).
The role of dynamic conformational ensembles in biomolecular recognition.
  Nat Chem Biol, 5, 789-796.  
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.  
18369189 C.J.McCleverty, L.Columbus, A.Kreusch, and S.A.Lesley (2008).
Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634.
  Protein Sci, 17, 869-877.
PDB codes: 2vkj 2vko
18571833 J.W.Simpkins, S.H.Yang, S.N.Sarkar, and V.Pearce (2008).
Estrogen actions on mitochondria--physiological and pathological implications.
  Mol Cell Endocrinol, 290, 51-59.  
18063580 K.Yamano, Y.Yatsukawa, M.Esaki, A.E.Hobbs, R.E.Jensen, and T.Endo (2008).
Tom20 and Tom22 share the common signal recognition pathway in mitochondrial protein import.
  J Biol Chem, 283, 3799-3807.  
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.