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PDBsum entry 1gnp

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protein ligands metals links
Gtp binding protein PDB id
1gnp
Jmol
Contents
Protein chain
166 a.a. *
Ligands
AGN
Metals
_MG
* Residue conservation analysis
PDB id:
1gnp
Name: Gtp binding protein
Title: X-ray crystal structure analysis of the catalytic domain of the oncogene product p21h-ras complexed with caged gtp and mant dgppnhp
Structure: C-h-ras p21 protein. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
2.70Å     R-factor:   0.193    
Authors: A.Scheidig,S.M.Franken,J.E.T.Corrie,G.P.Reid,A.Wittinghofer, E.F.Pai,R.S.Goody
Key ref:
A.J.Scheidig et al. (1995). X-ray crystal structure analysis of the catalytic domain of the oncogene product p21H-ras complexed with caged GTP and mant dGppNHp. J Mol Biol, 253, 132-150. PubMed id: 7473708 DOI: 10.1006/jmbi.1995.0541
Date:
11-May-95     Release date:   31-Jul-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas
Seq:
Struc:
189 a.a.
166 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     signal transduction   3 terms 
  Biochemical function     GTP binding     1 term  

 

 
DOI no: 10.1006/jmbi.1995.0541 J Mol Biol 253:132-150 (1995)
PubMed id: 7473708  
 
 
X-ray crystal structure analysis of the catalytic domain of the oncogene product p21H-ras complexed with caged GTP and mant dGppNHp.
A.J.Scheidig, S.M.Franken, J.E.Corrie, G.P.Reid, A.Wittinghofer, E.F.Pai, R.S.Goody.
 
  ABSTRACT  
 
The X-ray structures of the 1:1 complexes formed between p21H-ras (residues 1 to 166) and the nucleotides P3-1-(2-nitrophenyl)ethyl guanosine triphosphate ("caged GTP"; pure R- and S-diastereomers) and 3'-O-(N-methylanthraniloyl)-2'-deoxyguanosine 5'-(beta, gamma-imido)-triphosphate ("mant dG-ppNHp"), have been refined to an R-factor of 21.4% (R-caged GTP, 1.85 A resolution), 18.9% (S-caged GTP, 2.5 A resolution) and 17.6% (mant dGppNHp, 2.7 A resolution), respectively. Details of the structure determination, refinement and the structures themselves are presented. The overall structures of the complexes are identical in terms of the general organization of their secondary structure elements and are also identical to that reported for the analogous complex of p21H-ras with GppNHp. The binding of the GTP part is not significantly affected by the additional aromatic group (cage and mant, respectively) in contrast to the original observation on p21:caged GTP using the racemic mixture of R- and S-caged GTP. The main differences in the structures are observed in the region of loop L2 (residues Glu31 to Thr35) where the additional aromatic group attached to the nucleotide comes very close to the side-chain of Tyr32, including backbone displacements of 2.6 A, 2.2 A and 0.3 A for the residues from Glu31 to Thr35 for R-caged, S-caged GTP and mant dGppNHp, respectively. The refined structures provide additional data for the design of new nucleotide analogs and the importance of their stereochemistry as well as for the design of new mutant forms of p21H-ras for further biochemical investigations. The binding mode of mant dGppNHp reveals significant features for the understanding of the fluorescence signals observed in solution.
 
  Selected figure(s)  
 
Figure 10.
Figure 10. Stereo view of the molecular packing in the crystal. Crystal contacts of the reference molecule (I) with the 12 neighboring molecules (II to XIII). The molecules II to XIII are symmetry related to molecule I as described in the legend to Table 4. (a) View along the c-axis on the a,b-plane. (b) View perpendicular to the c-axis on the a,c-plane. The molecules X and XII are not displayed as their interaction with molecule I is equal to the interaction of molecule I to VIII and XI, respectively.
Figure 11.
Figure 11. Loop L2 (from residue 30 to 36) and mant dGppNHp of p21c':mant dGppNHp superimposed with the tyrosine Tyr32 (thick line) of p21c':GDP (Schlichting et al., 1990 and our unpublished results).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 253, 132-150) copyright 1995.  
  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.  
20973973 B.U.Klink, and A.J.Scheidig (2010).
New insight into the dynamic properties and the active site architecture of H-Ras p21 revealed by X-ray crystallography at very high resolution.
  BMC Struct Biol, 10, 38.  
20018869 G.M.Gasmi-Seabrook, C.B.Marshall, M.Cheung, B.Kim, F.Wang, Y.J.Jang, T.W.Mak, V.Stambolic, and M.Ikura (2010).
Real-time NMR study of guanine nucleotide exchange and activation of RhoA by PDZ-RhoGEF.
  J Biol Chem, 285, 5137-5145.  
20018863 M.T.Mazhab-Jafari, C.B.Marshall, M.Smith, G.M.Gasmi-Seabrook, V.Stambolic, R.Rottapel, B.G.Neel, and M.Ikura (2010).
Real-time NMR study of three small GTPases reveals that fluorescent 2'(3')-O-(N-methylanthraniloyl)-tagged nucleotides alter hydrolysis and exchange kinetics.
  J Biol Chem, 285, 5132-5136.  
17385754 C.Kötting, A.Kallenbach, Y.Suveyzdis, C.Eichholz, and K.Gerwert (2007).
Surface change of Ras enabling effector binding monitored in real time at atomic resolution.
  Chembiochem, 8, 781-787.  
16698776 B.U.Klink, R.S.Goody, and A.J.Scheidig (2006).
A newly designed microspectrofluorometer for kinetic studies on protein crystals in combination with x-ray diffraction.
  Biophys J, 91, 981-992.
PDB codes: 2ce2 2cl0 2cl6 2cl7 2clc 2cld 2evw
15878861 M.Neuspiel, R.Zunino, S.Gangaraju, P.Rippstein, and H.McBride (2005).
Activated mitofusin 2 signals mitochondrial fusion, interferes with Bax activation, and reduces susceptibility to radical induced depolarization.
  J Biol Chem, 280, 25060-25070.  
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.  
11707393 Y.H.Song, A.Marx, J.Müller, G.Woehlke, M.Schliwa, A.Krebs, A.Hoenger, and E.Mandelkow (2001).
Structure of a fast kinesin: implications for ATPase mechanism and interactions with microtubules.
  EMBO J, 20, 6213-6225.
PDB code: 1goj
11123913 I.M.Li de La Sierra, J.Gallay, M.Vincent, T.Bertrand, P.Briozzo, O.Bârzu, and A.M.Gilles (2000).
Substrate-induced fit of the ATP binding site of cytidine monophosphate kinase from Escherichia coli: time-resolved fluorescence of 3'-anthraniloyl-2'-deoxy-ADP and molecular modeling.
  Biochemistry, 39, 15870-15878.  
11063593 P.Gonzalo, B.Sontag, J.P.Lavergne, J.M.Jault, and J.P.Reboud (2000).
Evidence for a second nucleotide binding site in rat elongation factor eEF-2 specific for adenylic nucleotides.
  Biochemistry, 39, 13558-13564.  
10869438 S.N.Murthy, and L.Lorand (2000).
Nucleotide binding by the erythrocyte transglutaminase/Gh protein, probed with fluorescent analogs of GTP and GDP.
  Proc Natl Acad Sci U S A, 97, 7744-7747.  
10574788 A.J.Scheidig, C.Burmester, and R.S.Goody (1999).
The pre-hydrolysis state of p21(ras) in complex with GTP: new insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins.
  Structure, 7, 1311-1324.
PDB codes: 1ctq 1qra
  10482526 B.Lin, K.L.Covalle, and J.R.Maddock (1999).
The Caulobacter crescentus CgtA protein displays unusual guanine nucleotide binding and exchange properties.
  J Bacteriol, 181, 5825-5832.  
  10631985 M.G.Rudolph, T.J.Veit, and J.Reinstein (1999).
The novel fluorescent CDP-analogue (Pbeta)MABA-CDP is a specific probe for the NMP binding site of UMP/CMP kinase.
  Protein Sci, 8, 2697-2704.  
10359839 M.R.Ahmadian, T.Zor, D.Vogt, W.Kabsch, Z.Selinger, A.Wittinghofer, and K.Scheffzek (1999).
Guanosine triphosphatase stimulation of oncogenic Ras mutants.
  Proc Natl Acad Sci U S A, 96, 7065-7070.
PDB codes: 1clu 1rvd
9548760 J.Q.Cheng, W.Jiang, and D.D.Hackney (1998).
Interaction of mant-adenosine nucleotides and magnesium with kinesin.
  Biochemistry, 37, 5288-5295.  
9778365 J.Zhang, and C.R.Matthews (1998).
The role of ligand binding in the kinetic folding mechanism of human p21(H-ras) protein.
  Biochemistry, 37, 14891-14899.  
9665734 V.Cepus, A.J.Scheidig, R.S.Goody, and K.Gerwert (1998).
Time-resolved FTIR studies of the GTPase reaction of H-ras p21 reveal a key role for the beta-phosphate.
  Biochemistry, 37, 10263-10271.  
9312017 J.Cherfils, J.Ménétrey, G.Le Bras, I.Janoueix-Lerosey, J.de Gunzburg, J.R.Garel, and I.Auzat (1997).
Crystal structures of the small G protein Rap2A in complex with its substrate GTP, with GDP and with GTPgammaS.
  EMBO J, 16, 5582-5591.
PDB codes: 1kao 2rap
9116005 M.Yang, and T.S.Leyh (1997).
Altering the reaction coordinate of the ATP sulfurylase-GTPase reaction.
  Biochemistry, 36, 3270-3277.  
9242920 S.R.Sprang (1997).
G protein mechanisms: insights from structural analysis.
  Annu Rev Biochem, 66, 639-678.  
9230043 Y.Ito, K.Yamasaki, J.Iwahara, T.Terada, A.Kamiya, M.Shirouzu, Y.Muto, G.Kawai, S.Yokoyama, E.D.Laue, M.Wälchli, T.Shibata, S.Nishimura, and T.Miyazawa (1997).
Regional polysterism in the GTP-bound form of the human c-Ha-Ras protein.
  Biochemistry, 36, 9109-9119.
PDB code: 1aa9
8756686 M.Geyer, T.Schweins, C.Herrmann, T.Prisner, A.Wittinghofer, and H.R.Kalbitzer (1996).
Conformational transitions in p21ras and in its complexes with the effector protein Raf-RBD and the GTPase activating protein GAP.
  Biochemistry, 35, 10308-10320.  
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.