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PDBsum entry 1wrd
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protein Protein-protein interface(s) links
Protein transport/signaling protein PDB id
1wrd

 

 

 

 

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Contents
Protein chains
98 a.a. *
76 a.a. *
Waters ×289
* Residue conservation analysis
PDB id:
1wrd
Name: Protein transport/signaling protein
Title: Crystal structure of tom1 gat domain in complex with ubiquitin
Structure: Target of myb protein 1. Chain: a. Fragment: gat domain. Synonym: tom1. Engineered: yes. Ubiquitin. Chain: b
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Bos taurus. Cattle. Organism_taxid: 9913. Tissue: red blood cells
Biol. unit: Dimer (from PQS)
Resolution:
1.75Å     R-factor:   0.213     R-free:   0.259
Authors: M.Akutsu,M.Kawasaki,Y.Katoh,T.Shiba,Y.Yamaguchi,R.Kato,K.Kato, K.Nakayama,S.Wakatsuki
Key ref:
M.Akutsu et al. (2005). Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain. FEBS Lett, 579, 5385-5391. PubMed id: 16199040 DOI: 10.1016/j.febslet.2005.08.076
Date:
14-Oct-04     Release date:   11-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O60784  (TOM1_HUMAN) -  Target of Myb1 membrane trafficking protein from Homo sapiens
Seq:
Struc: 		492 a.a.
98 a.a.*
Protein chain
Pfam   ArchSchema ?
P0CH28  (UBC_BOVIN) -  Polyubiquitin-C from Bos taurus
Seq:
Struc: 		 
Seq:
Struc: 		690 a.a.
76 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.febslet.2005.08.076 FEBS Lett 579:5385-5391 (2005)
PubMed id: 16199040  
 
 
Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domain.
M.Akutsu, M.Kawasaki, Y.Katoh, T.Shiba, Y.Yamaguchi, R.Kato, K.Kato, K.Nakayama, S.Wakatsuki.
 
  ABSTRACT  
 
Tom1 (Target of Myb1) is suggested to be involved in the transport of ubiquitinated proteins, through the interaction of its GAT (GGA and Tom1) domain with ubiquitin. Here, we demonstrate that the three-helix bundle of Tom1-GAT has two ubiquitin-binding sites recognizing the hydrophobic Ile44 surface of ubiquitin. The complex crystal structure demonstrates that the first site is a hydrophobic patch on helices alpha1 and alpha2. NMR and biochemical data revealed that the N-terminal half of helix alpha3 of Tom1-GAT constitutes the second, stronger binding site. The double-sided ubiquitin binding enhances the efficiency of recognition of ubiquitinated proteins by Tom1.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. (A) Crystal structure of Tom1-GAT/ubiquitin complex, and (B) a view rotated by 90° about the horizontal axis. (C) Superposition of Tom1-GAT molecule (red), GGA1-GAT (blue) and GGA3-GAT (cyan), in the same view as (A). 		Figure 3.
Fig. 3. Ubiquitin-binding Site 1 of Tom1-GAT. (A) Stereo ribbon representation of the interface between Site 1 of Tom1-GAT (red) and ubiquitin (blue), in the same view as Fig. 1A. Side chains of Tom1-GAT and ubiquitin directly involved in the interactions are shown in ball-and-stick models with labels. The salt bridge between Glu256 and Arg42 is indicated by a red line. (B) The molecular surface of ubiquitin is shown with a ribbon drawing of GAT, in the same view as (A). Hydrophobic residues of ubiquitin are colored green. Residues participating in the interaction are labeled. (C) The molecular surface of GAT is shown with a line drawing of ubiquitin, in the view rotated 180° about the vertical axis relative to (A).
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2005, 579, 5385-5391) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20159559 M.G.Bomar, S.D'Souza, M.Bienko, I.Dikic, G.C.Walker, and P.Zhou (2010).
Unconventional ubiquitin recognition by the ubiquitin-binding motif within the Y family DNA polymerases iota and Rev1.
  Mol Cell, 37, 408-417.
PDB code: 2khu
20604899 T.Wang, N.S.Liu, L.F.Seet, and W.Hong (2010).
The emerging role of VHS domain-containing Tom1, Tom1L1 and Tom1L2 in membrane trafficking.
  Traffic, 11, 1119-1128.  
19129200 C.S.Chen, C.M.Nelson, D.Khauv, S.Bennett, E.S.Radisky, Y.Hirai, M.J.Bissell, and D.C.Radisky (2009).
Homology with vesicle fusion mediator syntaxin-1a predicts determinants of epimorphin/syntaxin-2 function in mammary epithelial morphogenesis.
  J Biol Chem, 284, 6877-6884.  
19773779 I.Dikic, S.Wakatsuki, and K.J.Walters (2009).
Ubiquitin-binding domains - from structures to functions.
  Nat Rev Mol Cell Biol, 10, 659-671.  
19183301 Y.Zwang, and Y.Yarden (2009).
Systems biology of growth factor-induced receptor endocytosis.
  Traffic, 10, 349-363.  
18343975 S.Girirajan, P.M.Hauck, S.Williams, C.N.Vlangos, B.B.Szomju, S.Solaymani-Kohal, P.D.Mosier, K.L.White, K.McCoy, and S.H.Elsea (2008).
Tom1l2 hypomorphic mice exhibit increased incidence of infections and tumors and abnormal immunologic response.
  Mamm Genome, 19, 246-262.  
17543868 G.Prag, H.Watson, Y.C.Kim, B.M.Beach, R.Ghirlando, G.Hummer, J.S.Bonifacino, and J.H.Hurley (2007).
The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting.
  Dev Cell, 12, 973-986.
PDB code: 2pjw
17494868 J.Wang, H.Q.Sun, E.Macia, T.Kirchhausen, H.Watson, J.S.Bonifacino, and H.L.Yin (2007).
PI4P promotes the recruitment of the GGA adaptor proteins to the trans-Golgi network and regulates their recognition of the ubiquitin sorting signal.
  Mol Biol Cell, 18, 2646-2655.  
17303403 V.Kirkin, and I.Dikic (2007).
Role of ubiquitin- and Ubl-binding proteins in cell signaling.
  Curr Opin Cell Biol, 19, 199-205.  
17125150 R.L.Rich, and D.G.Myszka (2006).
Survey of the year 2005 commercial optical biosensor literature.
  J Mol Recognit, 19, 478-534.  
16518384 S.L.Alam, and W.I.Sundquist (2006).
Two new structures of Ub-receptor complexes. U2.
  Nat Struct Mol Biol, 13, 186-188.  
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.

 

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