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PDBsum entry 1d5t
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protein ligands links
Hydrolase inhibitor PDB id
1d5t

 

 

 

 

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Contents
Protein chain
433 a.a. *
Ligands
SO4 ×2
Waters ×387
* Residue conservation analysis
PDB id:
1d5t
Name: Hydrolase inhibitor
Title: Guanine nucleotide dissociation inhibitor, alpha-isoform
Structure: Guanine nucleotide dissociation inhibitor. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.04Å     R-factor:   0.172     R-free:   0.208
Authors: L.Peng,K.Zeng,A.Heine,B.Moyer,S.E.Greasley,P.Kuhn,W.E.Balch, I.A.Wilson
Key ref: P.Luan et al. (2000). A new functional domain of guanine nucleotide dissociation inhibitor (alpha-GDI) involved in Rab recycling. Traffic, 1, 270-281. PubMed id: 11208110
Date:
11-Oct-99     Release date:   25-Oct-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21856  (GDIA_BOVIN) -  Rab GDP dissociation inhibitor alpha from Bos taurus
Seq:
Struc: 		447 a.a.
433 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
Traffic 1:270-281 (2000)
PubMed id: 11208110  
 
 
A new functional domain of guanine nucleotide dissociation inhibitor (alpha-GDI) involved in Rab recycling.
P.Luan, A.Heine, K.Zeng, B.Moyer, S.E.Greasely, P.Kuhn, W.E.Balch, I.A.Wilson.
 
  ABSTRACT  
 
Guanine nucleotide dissociation inhibitor (GDI) is a 55-kDa protein that functions in vesicular membrane transport to recycle Rab GTPases. We have now determined the crystal structure of bovine alpha-GDI at ultra-high resolution (1.04 A). Refinement at this resolution highlighted a region with high mobility of its main-chain residues. This corresponded to a surface loop in the primarily alpha-helical domain II at the base of alpha-GDI containing the previously uncharacterized sequence-conserved region (SCR) 3A. Site-directed mutagenesis showed that this mobile loop plays a crucial role in binding of GDI to membranes and extraction of membrane-bound Rab. This domain, referred to as the mobile effector loop, in combination with Rab-binding residues found in the multi-sheet domain I at the apex of alpha-GDI may provide flexibility for recycling of diverse Rab GTPases. We propose that conserved residues in domains I and II synergize to form the functional face of GDI, and that domain II mediates a critical step in Rab recycling during vesicle fusion.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18426803 A.Ignatev, S.Kravchenko, A.Rak, R.S.Goody, and O.Pylypenko (2008).
A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism.
  J Biol Chem, 283, 18377-18384.
PDB codes: 3cph 3cpi 3cpj
16687576 C.Y.Chen, and W.E.Balch (2006).
The Hsp90 chaperone complex regulates GDI-dependent Rab recycling.
  Mol Biol Cell, 17, 3494-3507.  
16395334 O.Pylypenko, A.Rak, T.Durek, S.Kushnir, B.E.Dursina, N.H.Thomae, A.T.Constantinescu, L.Brunsveld, A.Watzke, H.Waldmann, R.S.Goody, and K.Alexandrov (2006).
Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-mediated Rab recycling.
  EMBO J, 25, 13-23.
PDB code: 2bcg
16980382 Y.Ma, T.Kuno, A.Kita, T.Nabata, S.Uno, and R.Sugiura (2006).
Genetic evidence for phospholipid-mediated regulation of the Rab GDP-dissociation inhibitor in fission yeast.
  Genetics, 174, 1259-1271.  
15261679 M.C.Seabra, and C.Wasmeier (2004).
Controlling the location and activation of Rab GTPases.
  Curr Opin Cell Biol, 16, 451-457.  
15520808 S.Pfeffer, and D.Aivazian (2004).
Targeting Rab GTPases to distinct membrane compartments.
  Nat Rev Mol Cell Biol, 5, 886-896.  
14576435 A.Rak, O.Pylypenko, T.Durek, A.Watzke, S.Kushnir, L.Brunsveld, H.Waldmann, R.S.Goody, and K.Alexandrov (2003).
Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase.
  Science, 302, 646-650.
PDB code: 1ukv
12972569 C.Alory, and W.E.Balch (2003).
Molecular evolution of the Rab-escort-protein/guanine-nucleotide-dissociation-inhibitor superfamily.
  Mol Biol Cell, 14, 3857-3867.  
12620235 O.Pylypenko, A.Rak, R.Reents, A.Niculae, V.Sidorovitch, M.D.Cioaca, E.Bessolitsyna, N.H.Thomä, H.Waldmann, I.Schlichting, R.S.Goody, and K.Alexandrov (2003).
Structure of Rab escort protein-1 in complex with Rab geranylgeranyltransferase.
  Mol Cell, 11, 483-494.
PDB code: 1ltx
12623022 Y.An, Y.Shao, C.Alory, J.Matteson, T.Sakisaka, W.Chen, R.A.Gibbs, I.A.Wilson, and W.E.Balch (2003).
Geranylgeranyl switching regulates GDI-Rab GTPase recycling.
  Structure, 11, 347-357.
PDB code: 1lv0
12426384 T.Sakisaka, T.Meerlo, J.Matteson, H.Plutner, and W.E.Balch (2002).
Rab-alphaGDI activity is regulated by a Hsp90 chaperone complex.
  EMBO J, 21, 6125-6135.  
11489211 C.Alory, and W.E.Balch (2001).
Organization of the Rab-GDI/CHM superfamily: the functional basis for choroideremia disease.
  Traffic, 2, 532-543.  
11668674 C.S.Ricard, J.M.Jakubowski, J.W.Verbsky, M.A.Barbieri, W.M.Lewis, G.E.Fernandez, M.Vogel, C.Tsou, V.Prasad, P.D.Stahl, G.Waksman, and C.M.Cheney (2001).
Drosophila rab GDI mutants disrupt development but have normal Rab membrane extraction.
  Genesis, 31, 17-29.  
11447595 M.H.Brummer, P.Richard, L.Sundqvist, R.Väänänen, and S.Keränen (2001).
The GDI1 genes from Kluyveromyces lactis and Pichia pastoris: cloning and functional expression in Saccharomyces cerevisiae.
  Yeast, 18, 897-902.  
11239470 V.Cavalli, F.Vilbois, M.Corti, M.J.Marcote, K.Tamura, M.Karin, S.Arkinstall, and J.Gruenberg (2001).
The stress-induced MAP kinase p38 regulates endocytic trafficking via the GDI:Rab5 complex.
  Mol Cell, 7, 421-432.  
10893259 C.Alory, and W.E.Balch (2000).
Molecular basis for Rab prenylation.
  J Cell Biol, 150, 89.  
11208133 J.A.Ybe, D.E.Wakeham, F.M.Brodsky, and P.K.Hwang (2000).
Molecular structures of proteins involved in vesicle fusion.
  Traffic, 1, 474-479.  
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 codes are shown on the right.

 

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