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PDBsum entry 1elk
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protein Protein-protein interface(s) links
Endocytosis/exocytosis PDB id
1elk

 

 

 

 

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Contents
Protein chain
153 a.a. *
Waters ×377
* Residue conservation analysis
PDB id:
1elk
Name: Endocytosis/exocytosis
Title: Vhs domain of tom1 protein from h. Sapiens
Structure: Target of myb1. Chain: a, b. Fragment: vhs domain. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.50Å     R-factor:   0.193     R-free:   0.221
Authors: S.Misra,B.Beach,J.H.Hurley
Key ref:
S.Misra et al. (2000). Structure of the VHS domain of human Tom1 (target of myb 1): insights into interactions with proteins and membranes. Biochemistry, 39, 11282-11290. PubMed id: 10985773 DOI: 10.1021/bi0013546
Date:
13-Mar-00     Release date:   22-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O60784  (TOM1_HUMAN) -  Target of Myb1 membrane trafficking protein from Homo sapiens
Seq:
Struc: 		492 a.a.
153 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.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1021/bi0013546 Biochemistry 39:11282-11290 (2000)
PubMed id: 10985773  
 
 
Structure of the VHS domain of human Tom1 (target of myb 1): insights into interactions with proteins and membranes.
S.Misra, B.M.Beach, J.H.Hurley.
 
  ABSTRACT  
 
VHS domains are found at the N-termini of select proteins involved in intracellular membrane trafficking. We have determined the crystal structure of the VHS domain of the human Tom1 (target of myb 1) protein to 1.5 A resolution. The domain consists of eight helices arranged in a superhelix. The surface of the domain has two main features: (1) a basic patch on one side due to several conserved positively charged residues on helix 3 and (2) a negatively charged ridge on the opposite side, formed by residues on helix 2. We compare our structure to the recently obtained structure of tandem VHS-FYVE domains from Hrs [Mao, Y., Nickitenko, A., Duan, X., Lloyd, T. E., Wu, M. N., Bellen, H., and Quiocho, F. A. (2000) Cell 100, 447-456]. Key features of the interaction surface between the FYVE and VHS domains of Hrs, involving helices 2 and 4 of the VHS domain, are conserved in the VHS domain of Tom1, even though Tom1 does not have a FYVE domain. We also compare the structures of the VHS domains of Tom1 and Hrs to the recently obtained structure of the ENTH domain of epsin-1 [Hyman, J., Chen, H., Di Fiore, P. P., De Camilli, P., and Brünger, A. T. (2000) J. Cell Biol. 149, 537-546]. Comparison of the two VHS domains and the ENTH domain reveals a conserved surface, composed of helices 2 and 4, that is utilized for protein-protein interactions. In addition, VHS domain-containing proteins are often localized to membranes. We suggest that the conserved positively charged surface of helix 3 in VHS and ENTH domains plays a role in membrane binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
20150893 X.Ren, and J.H.Hurley (2010).
VHS domains of ESCRT-0 cooperate in high-avidity binding to polyubiquitinated cargo.
  EMBO J, 29, 1045-1054.
PDB code: 3ldz
  20054405 L.V.Omelyanchuk, J.A.Pertseva, S.S.Burns, and L.S.Chang (2009).
Evolution and Origin of HRS, a Protein Interacting with Merlin, the Neurofibromatosis 2 Gene Product.
  Gene Regul Syst Bio, 3, 143-157.  
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.  
17060447 N.LaRonde-LeBlanc, A.N.Santhanam, A.R.Baker, A.Wlodawer, and N.H.Colburn (2007).
Structural basis for inhibition of translation by the tumor suppressor Pdcd4.
  Mol Cell Biol, 27, 147-156.
PDB codes: 2iol 2ion 2ios 2nsz
16689637 J.H.Hurley, and S.D.Emr (2006).
The ESCRT complexes: structure and mechanism of a membrane-trafficking network.
  Annu Rev Biophys Biomol Struct, 35, 277-298.  
  16489693 M.Curlin, V.Lucić, and S.Gajović (2006).
Splice variant of mouse Stam2 mRNA in nervous and muscle tissue contains additional exon with stop codon within region coding for VHS domain.
  Croat Med J, 47, 16-24.  
16488176 V.Winter, and M.T.Hauser (2006).
Exploring the ESCRTing machinery in eukaryotes.
  Trends Plant Sci, 11, 115-123.  
15611048 R.Puertollano (2005).
Interactions of TOM1L1 with the multivesicular body sorting machinery.
  J Biol Chem, 280, 9258-9264.  
15496406 C.Gorbea, G.M.Goellner, K.Teter, R.K.Holmes, and M.Rechsteiner (2004).
Characterization of mammalian Ecm29, a 26 S proteasome-associated protein that localizes to the nucleus and membrane vesicles.
  J Biol Chem, 279, 54849-54861.  
14708007 J.S.Bonifacino (2004).
The GGA proteins: adaptors on the move.
  Nat Rev Mol Cell Biol, 5, 23-32.  
15056867 M.Yamakami, and H.Yokosawa (2004).
Tom1 (target of Myb 1) is a novel negative regulator of interleukin-1- and tumor necrosis factor-induced signaling pathways.
  Biol Pharm Bull, 27, 564-566.  
14555471 D.A.Bulik, M.Olczak, H.A.Lucero, B.C.Osmond, P.W.Robbins, and C.A.Specht (2003).
Chitin synthesis in Saccharomyces cerevisiae in response to supplementation of growth medium with glucosamine and cell wall stress.
  Eukaryot Cell, 2, 886-900.  
12972556 E.Mizuno, K.Kawahata, M.Kato, N.Kitamura, and M.Komada (2003).
STAM proteins bind ubiquitinated proteins on the early endosome via the VHS domain and ubiquitin-interacting motif.
  Mol Biol Cell, 14, 3675-3689.  
12767220 G.Zhu, P.Zhai, X.He, S.Terzyan, R.Zhang, A.Joachimiak, J.Tang, and X.C.Zhang (2003).
Crystal structure of the human GGA1 GAT domain.
  Biochemistry, 42, 6392-6399.
PDB code: 1oxz
14745135 K.Nakayama, and S.Wakatsuki (2003).
The structure and function of GGAs, the traffic controllers at the TGN sorting crossroads.
  Cell Struct Funct, 28, 431-442.  
12486728 M.Albrecht, D.Hoffmann, B.O.Evert, I.Schmitt, U.Wüllner, and T.Lengauer (2003).
Structural modeling of ataxin-3 reveals distant homology to adaptins.
  Proteins, 50, 355-370.  
14563850 M.Yamakami, T.Yoshimori, and H.Yokosawa (2003).
Tom1, a VHS domain-containing protein, interacts with tollip, ubiquitin, and clathrin.
  J Biol Chem, 278, 52865-52872.  
12388763 H.Dewar, D.T.Warren, F.C.Gardiner, C.G.Gourlay, N.Satish, M.R.Richardson, P.D.Andrews, and K.R.Ayscough (2002).
Novel proteins linking the actin cytoskeleton to the endocytic machinery in Saccharomyces cerevisiae.
  Mol Biol Cell, 13, 3646-3661.  
11796224 J.H.Hurley, D.E.Anderson, B.Beach, B.Canagarajah, Y.S.Ho, E.Jones, G.Miller, S.Misra, M.Pearson, L.Saidi, S.Suer, R.Trievel, and Y.Tsujishita (2002).
Structural genomics and signaling domains.
  Trends Biochem Sci, 27, 48-53.  
11545740 C.Mazza, M.Ohno, A.Segref, I.W.Mattaj, and S.Cusack (2001).
Crystal structure of the human nuclear cap binding complex.
  Mol Cell, 8, 383-396.
PDB code: 1h6k
11248547 J.H.Hurley, and T.Meyer (2001).
Subcellular targeting by membrane lipids.
  Curr Opin Cell Biol, 13, 146-152.  
  11694590 J.Hirst, M.R.Lindsay, and M.S.Robinson (2001).
GGAs: roles of the different domains and comparison with AP-1 and clathrin.
  Mol Biol Cell, 12, 3573-3588.  
11454451 M.S.Robinson, and J.S.Bonifacino (2001).
Adaptor-related proteins.
  Curr Opin Cell Biol, 13, 444-453.  
11301005 R.Puertollano, P.A.Randazzo, J.F.Presley, L.M.Hartnell, and J.S.Bonifacino (2001).
The GGAs promote ARF-dependent recruitment of clathrin to the TGN.
  Cell, 105, 93.  
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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