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PDBsum entry 2rgf

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protein links
Ras-binding domain PDB id
2rgf
Jmol
Contents
Protein chain
97 a.a. *
* Residue conservation analysis
PDB id:
2rgf
Name: Ras-binding domain
Title: Rbd of ral guanosine-nucleotide exchange factor (protein), nmr, 10 structures
Structure: Ralgef-rbd. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: human ralgef gene (ralgds). Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 10 models
Authors: M.Geyer,C.Herrmann,A.Wittinghofer,H.R.Kalbitzer
Key ref: M.Geyer et al. (1997). Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signalling. Nat Struct Biol, 4, 694-699. PubMed id: 9302994
Date:
13-Feb-97     Release date:   04-Mar-98    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q12967  (GNDS_HUMAN) -  Ral guanine nucleotide dissociation stimulator
Seq:
Struc:
 
Seq:
Struc:
914 a.a.
97 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     signal transduction   1 term 

 

 
Nat Struct Biol 4:694-699 (1997)
PubMed id: 9302994  
 
 
Structure of the Ras-binding domain of RalGEF and implications for Ras binding and signalling.
M.Geyer, C.Herrmann, S.Wohlgemuth, A.Wittinghofer, H.R.Kalbitzer.
 
  ABSTRACT  
 
The solution structure of the Ras-binding domain (RBD) of Ral guanine-nucleotide exchange factor RalGEF was solved by NMR spectroscopy. The overall structure is similar to that of Raf-RBD, another effector of Ras, although the sequence identity is only 13%. 15N chemical shifts changes in the complex of RalGEF-RBD with Ras indicate an interaction similar to the intermolecular beta-sheet observed for the complex between Ras and Raf-RBD.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19801192 G.Fuentes, and A.Valencia (2009).
Ras classical effectors: new tales from in silico complexes.
  Trends Biochem Sci, 34, 533-539.  
18786395 A.Schulte, B.Stolp, A.Schönichen, O.Pylypenko, A.Rak, O.T.Fackler, and M.Geyer (2008).
The human formin FHOD1 contains a bipartite structure of FH3 and GTPase-binding domains required for activation.
  Structure, 16, 1313-1323.
PDB code: 3dad
19096503 C.Kiel, D.Aydin, and L.Serrano (2008).
Association rate constants of ras-effector interactions are evolutionarily conserved.
  PLoS Comput Biol, 4, e1000245.  
18354782 L.E.Goldfinger (2008).
Choose your own path: specificity in Ras GTPase signaling.
  Mol Biosyst, 4, 293-299.  
17955183 F.H.Schumann, H.Riepl, T.Maurer, W.Gronwald, K.P.Neidig, and H.R.Kalbitzer (2007).
Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions.
  J Biomol NMR, 39, 275-289.  
17295314 S.Tomić, B.Bertosa, T.Wang, and R.C.Wade (2007).
COMBINE analysis of the specificity of binding of Ras proteins to their effectors.
  Proteins, 67, 435-447.  
17136423 W.Gronwald, K.Brunner, R.Kirchhöfer, J.Trenner, K.P.Neidig, and H.R.Kalbitzer (2007).
AUREMOL-RFAC-3D, combination of R-factors and their use for automated quality assessment of protein solution structures.
  J Biomol NMR, 37, 15-30.  
16856944 H.M.Fang, and Y.Wang (2006).
RA domain-mediated interaction of Cdc35 with Ras1 is essential for increasing cellular cAMP level for Candida albicans hyphal development.
  Mol Microbiol, 61, 484-496.  
16800891 K.Brunner, W.Gronwald, J.M.Trenner, K.P.Neidig, and H.R.Kalbitzer (2006).
A general method for the unbiased improvement of solution NMR structures by the use of related X-ray data, the AUREMOL-ISIC algorithm.
  BMC Struct Biol, 6, 14.  
16928684 M.Kukimoto-Niino, T.Takagi, R.Akasaka, K.Murayama, T.Uchikubo-Kamo, T.Terada, M.Inoue, S.Watanabe, A.Tanaka, Y.Hayashizaki, T.Kigawa, M.Shirouzu, and S.Yokoyama (2006).
Crystal structure of the RUN domain of the RAP2-interacting protein x.
  J Biol Chem, 281, 31843-31853.
PDB codes: 2cxf 2cxl 2dwg 2dwk
16235217 M.Spoerner, T.F.Prisner, M.Bennati, M.M.Hertel, N.Weiden, T.Schweins, and H.R.Kalbitzer (2005).
Conformational states of human H-Ras detected by high-field EPR, ENDOR, and 31P NMR spectroscopy.
  Magn Reson Chem, 43, S74-S83.  
15994326 M.Ye, F.Shima, S.Muraoka, J.Liao, H.Okamoto, M.Yamamoto, A.Tamura, N.Yagi, T.Ueki, and T.Kataoka (2005).
Crystal structure of M-Ras reveals a GTP-bound "off" state conformation of Ras family small GTPases.
  J Biol Chem, 280, 31267-31275.
PDB codes: 1x1r 1x1s
15653425 E.J.Helmreich (2004).
Structural flexibility of small GTPases. Can it explain their functional versatility?
  Biol Chem, 385, 1121-1136.  
12714997 C.A.Moores, F.Francis, M.Perderiset, and A.Houdusse (2003).
A double-take on MAPs.
  Nat Struct Biol, 10, 314-316.  
12581669 C.Herrmann (2003).
Ras-effector interactions: after one decade.
  Curr Opin Struct Biol, 13, 122-129.  
14514689 D.Owen, P.N.Lowe, D.Nietlispach, C.E.Brosnan, D.Y.Chirgadze, P.J.Parker, T.L.Blundell, and H.R.Mott (2003).
Molecular dissection of the interaction between the small G proteins Rac1 and RhoA and protein kinase C-related kinase 1 (PRK1).
  J Biol Chem, 278, 50578-50587.
PDB code: 1urf
14556626 M.Geyer, C.Wilde, J.Selzer, K.Aktories, and H.R.Kalbitzer (2003).
Glucosylation of Ras by Clostridium sordellii lethal toxin: consequences for effector loop conformations observed by NMR spectroscopy.
  Biochemistry, 42, 11951-11959.  
11723130 M.Kido, F.Shima, T.Satoh, T.Asato, K.Kariya, and T.Kataoka (2002).
Critical function of the Ras-associating domain as a primary Ras-binding site for regulation of Saccharomyces cerevisiae adenylyl cyclase.
  J Biol Chem, 277, 3117-3123.  
11748241 T.Linnemann, C.Kiel, P.Herter, and C.Herrmann (2002).
The activation of RalGDS can be achieved independently of its Ras binding domain. Implications of an activation mechanism in Ras effector specificity and signal distribution.
  J Biol Chem, 277, 7831-7837.  
11784866 Y.Wang, R.T.Waldron, A.Dhaka, A.Patel, M.M.Riley, E.Rozengurt, and J.Colicelli (2002).
The RAS effector RIN1 directly competes with RAF and is regulated by 14-3-3 proteins.
  Mol Cell Biol, 22, 916-926.  
11438672 G.Buchwald, E.Hostinova, M.G.Rudolph, A.Kraemer, A.Sickmann, H.E.Meyer, K.Scheffzek, and A.Wittinghofer (2001).
Conformational switch and role of phosphorylation in PAK activation.
  Mol Cell Biol, 21, 5179-5189.  
11709168 K.Scheffzek, P.Grünewald, S.Wohlgemuth, W.Kabsch, H.Tu, M.Wigler, A.Wittinghofer, and C.Herrmann (2001).
The Ras-Byr2RBD complex: structural basis for Ras effector recognition in yeast.
  Structure, 9, 1043-1050.
PDB code: 1k8r
11320243 M.Spoerner, C.Herrmann, I.R.Vetter, H.R.Kalbitzer, and A.Wittinghofer (2001).
Dynamic properties of the Ras switch I region and its importance for binding to effectors.
  Proc Natl Acad Sci U S A, 98, 4944-4949.
PDB code: 1iaq
11369865 W.Gronwald, E.Brunner, F.Huber, M.Wenzler, C.Herrmann, and H.R.Kalbitzer (2001).
Overcoming the problems associated with poor spectra quality of the protein kinase Byr2 using residual dipolar couplings.
  Protein Sci, 10, 1260-1263.  
11709167 W.Gronwald, F.Huber, P.Grünewald, M.Spörner, S.Wohlgemuth, C.Herrmann, and H.R.Kalbitzer (2001).
Solution structure of the Ras binding domain of the protein kinase Byr2 from Schizosaccharomyces pombe.
  Structure, 9, 1029-1041.
PDB code: 1i35
  10386876 A.M.Wyndham, R.T.Baker, and G.Chelvanayagam (1999).
The Ubp6 family of deubiquitinating enzymes contains a ubiquitin-like domain: SUb.
  Protein Sci, 8, 1268-1275.  
10364219 B.Bauer, G.Mirey, I.R.Vetter, J.A.García-Ranea, A.Valencia, A.Wittinghofer, J.H.Camonis, and R.H.Cool (1999).
Effector recognition by the small GTP-binding proteins Ras and Ral.
  J Biol Chem, 274, 17763-17770.  
  10210183 J.Zeng, M.Fridman, H.Maruta, H.R.Treutlein, and T.Simonson (1999).
Protein-protein recognition: an experimental and computational study of the R89K mutation in Raf and its effect on Ras binding.
  Protein Sci, 8, 50-64.  
10213614 M.Shirouzu, K.Hashimoto, A.Kikuchi, and S.Yokoyama (1999).
Double-mutant analysis of the interaction of Ras with the Ras-binding domain of RGL.
  Biochemistry, 38, 5103-5110.  
10072355 R.M.Wolthuis, and J.L.Bos (1999).
Ras caught in another affair: the exchange factors for Ral.
  Curr Opin Genet Dev, 9, 112-117.  
10619026 R.Maesaki, K.Ihara, T.Shimizu, S.Kuroda, K.Kaibuchi, and T.Hakoshima (1999).
The structural basis of Rho effector recognition revealed by the crystal structure of human RhoA complexed with the effector domain of PKN/PRK1.
  Mol Cell, 4, 793-803.
PDB code: 1cxz
10224125 T.Linnemann, M.Geyer, B.K.Jaitner, C.Block, H.R.Kalbitzer, A.Wittinghofer, and C.Herrmann (1999).
Thermodynamic and kinetic characterization of the interaction between the Ras binding domain of AF6 and members of the Ras subfamily.
  J Biol Chem, 274, 13556-13562.  
10085114 V.Nancy, R.M.Wolthuis, M.F.de Tand, I.Janoueix-Lerosey, J.L.Bos, and J.de Gunzburg (1999).
Identification and characterization of potential effector molecules of the Ras-related GTPase Rap2.
  J Biol Chem, 274, 8737-8745.  
9753431 D.Esser, B.Bauer, R.M.Wolthuis, A.Wittinghofer, R.H.Cool, and P.Bayer (1998).
Structure determination of the Ras-binding domain of the Ral-specific guanine nucleotide exchange factor Rlf.
  Biochemistry, 37, 13453-13462.
PDB code: 1rlf
9628477 L.Huang, F.Hofer, G.S.Martin, and S.H.Kim (1998).
Structural basis for the interaction of Ras with RalGDS.
  Nat Struct Biol, 5, 422-426.
PDB code: 1lfd
9660763 M.G.Rudolph, P.Bayer, A.Abo, J.Kuhlmann, I.R.Vetter, and A.Wittinghofer (1998).
The Cdc42/Rac interactive binding region motif of the Wiskott Aldrich syndrome protein (WASP) is necessary but not sufficient for tight binding to Cdc42 and structure formation.
  J Biol Chem, 273, 18067-18076.  
9553071 M.Ohnishi, Y.Yamawaki-Kataoka, K.Kariya, M.Tamada, C.D.Hu, and T.Kataoka (1998).
Selective inhibition of Ras interaction with its particular effector by synthetic peptides corresponding to the Ras effector region.
  J Biol Chem, 273, 10210-10215.  
9516482 M.Shirouzu, K.Morinaka, S.Koyama, C.D.Hu, N.Hori-Tamura, T.Okada, K.Kariya, T.Kataoka, A.Kikuchi, and S.Yokoyama (1998).
Interactions of the amino acid residue at position 31 of the c-Ha-Ras protein with Raf-1 and RalGDS.
  J Biol Chem, 273, 7737-7742.  
9434896 M.Geyer, and A.Wittinghofer (1997).
GEFs, GAPs, GDIs and effectors: taking a closer (3D) look at the regulation of Ras-related GTP-binding proteins.
  Curr Opin Struct Biol, 7, 786-792.  
9434906 S.R.Sprang (1997).
G proteins, effectors and GAPs: structure and mechanism.
  Curr Opin Struct Biol, 7, 849-856.  
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.