PDBsum entry 1ky2

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Endocytosis/exocytosis PDB id
Protein chain
180 a.a. *
Waters ×240
* Residue conservation analysis
PDB id:
Name: Endocytosis/exocytosis
Title: Gppnhp-bound ypt7p at 1.6 a resolution
Structure: Gtp-binding protein ypt7p. Chain: a. Fragment: gtpase domain. Synonym: gtp-binding protein ypt7. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ypt7. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.60Å     R-factor:   0.193     R-free:   0.249
Authors: A.-T.Constantinescu,A.Rak,A.J.Scheidig
Key ref:
A.T.Constantinescu et al. (2002). Rab-subfamily-specific regions of Ypt7p are structurally different from other RabGTPases. Structure, 10, 569-579. PubMed id: 11937061 DOI: 10.1016/S0969-2126(02)00737-2
02-Feb-02     Release date:   05-Jun-02    
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Protein chain
Pfam   ArchSchema ?
P32939  (YPT7_YEAST) -  GTP-binding protein YPT7
208 a.a.
180 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     signal transduction   6 terms 
  Biochemical function     GTP binding     2 terms  


DOI no: 10.1016/S0969-2126(02)00737-2 Structure 10:569-579 (2002)
PubMed id: 11937061  
Rab-subfamily-specific regions of Ypt7p are structurally different from other RabGTPases.
A.T.Constantinescu, A.Rak, K.Alexandrov, H.Esters, R.S.Goody, A.J.Scheidig.
The GTPase Ypt7p from S. cerevisiae is involved in late endosome-to-vacuole transport and homotypic vacuole fusion. We present crystal structures of the GDP- and GppNHp-bound conformation of Ypt7p solved at 1.35 and 1.6 A resolution, respectively. Despite the similarity of the overall structure to other Ypt/Rab proteins, Ypt7p displays small but significant differences. The Ypt7p-specific residues Tyr33 and Tyr37 cause a difference in the main chain trace of the RabSF2 region and form a characteristic surface epitope. Ypt7p*GppNHp does not display the helix alpha2, characteristic of the Ras-superfamily, but instead possess an extended loop L4/L5. Due to insertions in loops L3 and L7, the neighboring RabSF1 and RabSF4 regions are different in their conformations to those of other Ypt/Rab proteins.
  Selected figure(s)  
Figure 3.
Figure 3. Molecular Surface Representation of Ypt7pDifferences in surface topology and charge distribution between the GppNHp-bound form of Ypt7p (A) and Ypt51p (B). The view is related to the view of Figure 1 and Figure 2 by a 90 rotation. The regions with major structural differences are labeled. The molecular surface colored according to the electrostatic potential was calculated with the program GRASP [39].
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 569-579) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20534488 A.Mishra, S.Eathiraj, S.Corvera, and D.G.Lambright (2010).
Structural basis for Rab GTPase recognition and endosome tethering by the C2H2 zinc finger of Early Endosomal Autoantigen 1 (EEA1).
  Proc Natl Acad Sci U S A, 107, 10866-10871.
PDB code: 3mjh
19453973 J.Kashiwazaki, T.Iwaki, K.Takegawa, C.Shimoda, and T.Nakamura (2009).
Two fission yeast rab7 homologs, ypt7 and ypt71, play antagonistic roles in the regulation of vacuolar morphology.
  Traffic, 10, 912-924.  
19522756 M.T.Lee, A.Mishra, and D.G.Lambright (2009).
Structural mechanisms for regulation of membrane traffic by rab GTPases.
  Traffic, 10, 1377-1389.  
17183369 M.F.Kleijnen, D.S.Kirkpatrick, and S.P.Gygi (2007).
The ubiquitin-proteasome system regulates membrane fusion of yeast vacuoles.
  EMBO J, 26, 275-287.  
16790928 I.Garcia-Saez, S.Tcherniuk, and F.Kozielski (2006).
The structure of human neuronal Rab6B in the active and inactive form.
  Acta Crystallogr D Biol Crystallogr, 62, 725-733.
PDB codes: 2fe4 2ffq
17031879 L.Brunsveld, J.Kuhlmann, K.Alexandrov, A.Wittinghofer, R.S.Goody, and H.Waldmann (2006).
Lipidated ras and rab peptides and proteins--synthesis, structure, and function.
  Angew Chem Int Ed Engl, 45, 6622-6646.  
15468317 A.Golovin, D.Dimitropoulos, T.Oldfield, A.Rachedi, and K.Henrick (2005).
MSDsite: a database search and retrieval system for the analysis and viewing of bound ligands and active sites.
  Proteins, 58, 190-199.  
15785799 A.Watzke, L.Brunsveld, T.Durek, K.Alexandrov, A.Rak, R.S.Goody, and H.Waldmann (2005).
Chemical biology of protein lipidation: semi-synthesis and structure elucidation of prenylated RabGTPases.
  Org Biomol Chem, 3, 1157-1164.  
15746102 S.R.Pfeffer (2005).
Structural clues to Rab GTPase functional diversity.
  J Biol Chem, 280, 15485-15488.  
14978301 C.Blouin, D.Butt, and A.J.Roger (2004).
Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain.
  Protein Sci, 13, 608-616.  
15378032 G.Zhu, P.Zhai, J.Liu, S.Terzyan, G.Li, and X.C.Zhang (2004).
Structural basis of Rab5-Rabaptin5 interaction in endocytosis.
  Nat Struct Mol Biol, 11, 975-983.
PDB codes: 1tu3 1tu4
14993700 J.G.Wittmann, and M.G.Rudolph (2004).
Purification, crystallization and preliminary X-ray analysis of the GTP-binding protein Rab9 implicated in endosome-to-TGN vesicle trafficking.
  Acta Crystallogr D Biol Crystallogr, 60, 580-582.  
15263003 L.Chen, E.DiGiammarino, X.E.Zhou, Y.Wang, D.Toh, T.W.Hodge, and E.J.Meehan (2004).
High resolution crystal structure of human Rab9 GTPase: a novel antiviral drug target.
  J Biol Chem, 279, 40204-40208.
PDB code: 1wms
14699104 S.Pasqualato, F.Senic-Matuglia, L.Renault, B.Goud, J.Salamero, and J.Cherfils (2004).
The structural GDP/GTP cycle of Rab11 reveals a novel interface involved in the dynamics of recycling endosomes.
  J Biol Chem, 279, 11480-11488.
PDB codes: 1oiv 1oiw
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.