PDBsum entry 1clu

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Hydrolase PDB id
Protein chain
160 a.a. *
Waters ×46
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: H-ras complexed with diaminobenzophenone-beta,gamma-imido- gtp
Structure: Transforming protein p21/h-ras-1. Chain: a. Fragment: catalytic domain, residues 1 - 166. Synonym: h-ras, p21h-ras, p21ras. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: h-ras-1
Biol. unit: Monomer (from PDB file)
1.70Å     R-factor:   0.203     R-free:   0.261
Authors: M.R.Ahmadian,T.Zor,D.Vogt,W.Kabsch,Z.Selinger, A.Wittinghofer,K.Scheffzek
Key ref:
M.R.Ahmadian et al. (1999). Guanosine triphosphatase stimulation of oncogenic Ras mutants. Proc Natl Acad Sci U S A, 96, 7065-7070. PubMed id: 10359839 DOI: 10.1073/pnas.96.12.7065
03-May-99     Release date:   28-May-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas
189 a.a.
160 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     signal transduction   4 terms 
  Biochemical function     GTP binding     1 term  


DOI no: 10.1073/pnas.96.12.7065 Proc Natl Acad Sci U S A 96:7065-7070 (1999)
PubMed id: 10359839  
Guanosine triphosphatase stimulation of oncogenic Ras mutants.
M.R.Ahmadian, T.Zor, D.Vogt, W.Kabsch, Z.Selinger, A.Wittinghofer, K.Scheffzek.
Interest in the guanosine triphosphatase (GTPase) reaction of Ras as a molecular drug target stems from the observation that, in a large number of human tumors, Ras is characteristically mutated at codons 12 or 61, more rarely 13. Impaired GTPase activity, even in the presence of GTPase activating proteins, has been found to be the biochemical reason behind the oncogenicity of most Gly12/Gln61 mutations, thus preventing Ras from being switched off. Therefore, these oncogenic Ras mutants remain constitutively activated and contribute to the neoplastic phenotype of tumor cells. Here, we show that the guanosine 5'-triphosphate (GTP) analogue diaminobenzophenone-phosphoroamidate-GTP (DABP-GTP) is hydrolyzed by wild-type Ras but more efficiently by frequently occurring oncogenic Ras mutants, to yield guanosine 5'-diphosphate-bound inactive Ras and DABP-Pi. The reaction is independent of the presence of Gln61 and is most dramatically enhanced with Gly12 mutants. Thus, the defective GTPase reaction of the oncogenic Ras mutants can be rescued by using DABP-GTP instead of GTP, arguing that the GTPase switch of Ras is not irreversibly damaged. An exocyclic aromatic amino group of DABP-GTP is critical for the reaction and bypasses the putative rate-limiting step of the intrinsic Ras GTPase reaction. The crystal structures of Ras-bound DABP-beta,gamma-imido-GTP show a disordered switch I and identify the Gly12/Gly13 region as the hydrophobic patch to accommodate the DABP-moiety. The biochemical and structural studies help to define the requirements for the design of anti-Ras drugs aimed at the blocked GTPase reaction.
  Selected figure(s)  
Figure 1.
Fig. 1. Chemical structure of the GTP-phosphonoamidate derivatives. MABP, monoaminobenzophenone; PMA, phenylene-monoamine.
Figure 5.
Fig. 5. Solvent isotope effect of the GTPase and DABP-GTPase reaction. W32Ras was incubated with DABP-GTP in either H[2]O or D[2]O as indicated. The reaction was monitored by the fluorescence increase as before. The data were analyzed by single exponentials.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20949621 L.Gremer, T.Merbitz-Zahradnik, R.Dvorsky, I.C.Cirstea, C.P.Kratz, M.Zenker, A.Wittinghofer, and M.R.Ahmadian (2011).
Germline KRAS mutations cause aberrant biochemical and physical properties leading to developmental disorders.
  Hum Mutat, 32, 33-43.  
19995790 L.Gremer, A.De Luca, T.Merbitz-Zahradnik, B.Dallapiccola, S.Morlot, M.Tartaglia, K.Kutsche, M.R.Ahmadian, and G.Rosenberger (2010).
Duplication of Glu37 in the switch I region of HRAS impairs effector/GAP binding and underlies Costello syndrome by promoting enhanced growth factor-dependent MAPK and AKT activation.
  Hum Mol Genet, 19, 790-802.  
19321438 V.B.Kurella, J.M.Richard, C.L.Parke, L.F.Lecour, H.D.Bellamy, and D.K.Worthylake (2009).
Crystal structure of the GTPase-activating protein-related domain from IQGAP1.
  J Biol Chem, 284, 14857-14865.
PDB code: 3fay
18713003 L.Gremer, B.Gilsbach, M.R.Ahmadian, and A.Wittinghofer (2008).
Fluoride complexes of oncogenic Ras mutants to study the Ras-RasGap interaction.
  Biol Chem, 389, 1163-1171.  
18835035 N.Kotecha, N.J.Flores, J.M.Irish, E.F.Simonds, D.S.Sakai, S.Archambeault, E.Diaz-Flores, M.Coram, K.M.Shannon, G.P.Nolan, and M.L.Loh (2008).
Single-cell profiling identifies aberrant STAT5 activation in myeloid malignancies with specific clinical and biologic correlates.
  Cancer Cell, 14, 335-343.  
17330901 M.Kaneda, S.Masuda, T.Tomohiro, and Y.Hatanaka (2007).
A simple and efficient photoaffinity method for proteomics of GTP-binding proteins.
  Chembiochem, 8, 595-598.  
16307476 A.Eberth, R.Dvorsky, C.F.Becker, A.Beste, R.S.Goody, and M.R.Ahmadian (2005).
Monitoring the real-time kinetics of the hydrolysis reaction of guanine nucleotide-binding proteins.
  Biol Chem, 386, 1105-1114.  
16209721 E.G.Reynaud, M.A.Andrade, F.Bonneau, T.B.Ly, M.Knop, K.Scheffzek, and R.Pepperkok (2005).
Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.
  BMC Biol, 3, 21.  
16117800 G.A.Khan, G.Bhattacharya, P.C.Mailander, J.L.Meza, L.A.Hansen, and D.Chakravarti (2005).
Harvey-ras gene expression and epidermal cell proliferation in dibenzo[a,l]pyrene-treated early preneoplastic SENCAR mouse skin.
  J Invest Dermatol, 125, 567-574.  
15661535 K.Walker, and M.F.Olson (2005).
Targeting Ras and Rho GTPases as opportunities for cancer therapeutics.
  Curr Opin Genet Dev, 15, 62-68.  
16869784 P.Rodriguez-Viciana, O.Tetsu, K.Oda, J.Okada, K.Rauen, and F.McCormick (2005).
Cancer targets in the Ras pathway.
  Cold Spring Harb Symp Quant Biol, 70, 461-467.  
14757535 A.M.John, N.S.Thomas, G.J.Mufti, and R.A.Padua (2004).
Targeted therapies in myeloid leukemia.
  Semin Cancer Biol, 14, 41-62.  
15175044 F.Fellenberg, T.B.Hartmann, R.Dummer, D.Usener, D.Schadendorf, and S.Eichmüller (2004).
GBP-5 splicing variants: New guanylate-binding proteins with tumor-associated expression and antigenicity.
  J Invest Dermatol, 122, 1510-1517.  
14973186 J.Korlach, D.W.Baird, A.A.Heikal, K.R.Gee, G.R.Hoffman, and W.W.Webb (2004).
Spontaneous nucleotide exchange in low molecular weight GTPases by fluorescently labeled gamma-phosphate-linked GTP analogs.
  Proc Natl Acad Sci U S A, 101, 2800-2805.  
15457534 L.Soulère, C.Aldrich, O.Daumke, R.Gail, L.Kissau, A.Wittinghofer, and H.Waldmann (2004).
Synthesis of GTP-derived Ras ligands.
  Chembiochem, 5, 1448-1453.  
12704243 C.F.Becker, C.L.Hunter, R.Seidel, S.B.Kent, R.S.Goody, and M.Engelhard (2003).
Total chemical synthesis of a functional interacting protein pair: the protooncogene H-Ras and the Ras-binding domain of its effector c-Raf1.
  Proc Natl Acad Sci U S A, 100, 5075-5080.  
12509763 J.Downward (2003).
Targeting RAS signalling pathways in cancer therapy.
  Nat Rev Cancer, 3, 11-22.  
12535206 J.Halaschek-Wiener, Y.Kloog, V.Wacheck, and B.Jansen (2003).
Farnesyl thiosalicylic acid chemosensitizes human melanoma in vivo.
  J Invest Dermatol, 120, 109-115.  
12778136 M.Malumbres, and M.Barbacid (2003).
RAS oncogenes: the first 30 years.
  Nat Rev Cancer, 3, 459-465.  
12084068 M.Stumber, C.Herrmann, S.Wohlgemuth, H.R.Kalbitzer, W.Jahn, and M.Geyer (2002).
Synthesis, characterization and application of two nucleoside triphosphate analogues, GTPgammaNH(2) and GTPgammaF.
  Eur J Biochem, 269, 3270-3278.  
11306349 C.F.Becker, C.L.Hunter, R.P.Seidel, S.B.Kent, R.S.Goody, and M.Engelhard (2001).
A sensitive fluorescence monitor for the detection of activated Ras: total chemical synthesis of site-specifically labeled Ras binding domain of c-Raf1 immobilized on a surface.
  Chem Biol, 8, 243-252.  
11246021 M.Kosloff, and Z.Selinger (2001).
Substrate assisted catalysis -- application to G proteins.
  Trends Biochem Sci, 26, 161-166.  
11828490 R.Gail, B.Costisella, M.R.Ahmadian, and A.Wittinghofer (2001).
Ras-mediated cleavage of a GTP analogue by a novel mechanism.
  Chembiochem, 2, 570-575.  
11566135 S.Padmanabhan, and D.M.Freymann (2001).
The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase.
  Structure, 9, 859-867.
PDB codes: 1jpj 1jpn
11102795 F.McCormick (2000).
Small-molecule inhibitors of cell signaling.
  Curr Opin Biotechnol, 11, 593-597.  
10937867 M.Sprinzl, S.Brock, Y.Huang, P.Milovnik, M.Nanninga, M.Nesper-Brock, H.Rütthard, and K.Szkaradkiewicz (2000).
Regulation of GTPases in the bacterial translation machinery.
  Biol Chem, 381, 367-375.  
11006529 Y.Kloog, and A.D.Cox (2000).
RAS inhibitors: potential for cancer therapeutics.
  Mol Med Today, 6, 398-402.  
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.