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PDBsum entry 1jah

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protein ligands metals links
Gtp-binding PDB id
1jah
Jmol
Contents
Protein chain
166 a.a. *
Ligands
GCP
Metals
_MG
Waters ×25
* Residue conservation analysis
PDB id:
1jah
Name: Gtp-binding
Title: H-ras p21 protein mutant g12p, complexed with guanosine-5'- [beta,gamma-methylene] triphosphate and magnesium
Structure: C-ha-ras. Chain: a. Fragment: catalytic domain, residues 1 - 166. Synonym: g-domain. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: h-ras-1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.220     R-free:   0.290
Authors: T.Schweins,K.Scheffzek,R.Assheuer,A.Wittinghofer
Key ref:
T.Schweins et al. (1997). The role of the metal ion in the p21ras catalysed GTP-hydrolysis: Mn2+ versus Mg2+. J Mol Biol, 266, 847-856. PubMed id: 9102473 DOI: 10.1006/jmbi.1996.0814
Date:
15-Dec-96     Release date:   23-Jul-97    
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
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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.1996.0814 J Mol Biol 266:847-856 (1997)
PubMed id: 9102473  
 
 
The role of the metal ion in the p21ras catalysed GTP-hydrolysis: Mn2+ versus Mg2+.
T.Schweins, K.Scheffzek, R.Assheuer, A.Wittinghofer.
 
  ABSTRACT  
 
GTP and ATP hydrolysing proteins have an absolute requirement for a divalent cation, which is usually Mg2+, as a cofactor in the enzymatic reaction. Other phosphoryl transfer enzymes employ more than one divalent ion for the enzymatic reaction. It is shown here for p21ras, a well studied example of GTP hydrolysing proteins, that the GTP-hydrolysis rate is significantly faster if Mg2+ is replaced by Mn2+, both in the presence or absence of its GTPase-activating protein Ras-GAP. This effect is not due to a different stoichiometry of metal ion binding, since one metal ion is sufficient for full enzymatic activity. To determine the role of the metal ion, the crystal structure of p21(G12P). GppCp complexed with Mn2+ was determined and shown to be very similar to the corresponding p21(G12P). GppCp.Mg2+ structure. Especially the coordination sphere around the metal ions is very similar, and no second metal ion binding site could be detected, consistent with the assumption that one metal ion is sufficient for GTP hydrolysis. In order to explain the biochemical differences, we analysed the GTPase reaction mechanism with a linear free energy relationships approach. The result suggests that the reaction mechanism is not changed with Mn2+ but that the transition metal ion Mn2+ shifts the pKa of the gamma-phosphate by almost half a unit and increases the reaction rate due to an increase in the basicity of GTP acting as the general base. This suggests that the intrinsic GTPase reaction could be an attractive target for anti-cancer drug design. By using Rap1A and Ran, we show that the acceleration of the GTPase by Mn2+ appears to be a general phenomenon of GTP-binding proteins.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Location of Mn 2+ in the crystal structure of the p21(G12P) delta GppCp delta Mn complex. The crystal structures of p21(G12P) delta GppCp with either Mn 2+ (using standard colours) or Mg 2+ (blue) are superimposed on each other together with the difference-Fourier map (FoMn - FoMg) (Program FOFO, W.Kabsch, unpublished) contoured at either 80% (red) or 30% (blue) of the maximum.
Figure 6.
Figure 6. Stimulation of the Ran-GTPase by Mn 2+ : 200 mM Ran-GTP in the presence of stoichiometric amounts of either Mg 2+ or Mn 2+ were incubated and analysed for GTP hydrolysis as for the results in Figure 1. The data were fitted to single exponetial functions.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 266, 847-856) copyright 1997.  
  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.  
20064164 D.Guymer, J.Maillard, M.F.Agacan, C.A.Brearley, and F.Sargent (2010).
Intrinsic GTPase activity of a bacterial twin-arginine translocation proofreading chaperone induced by domain swapping.
  FEBS J, 277, 511-525.  
18697921 M.D.Smith, R.Mehdizadeh, J.E.Olive, and R.A.Collins (2008).
The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a.
  RNA, 14, 1942-1949.  
19001421 T.Bionda, P.Koenig, M.Oreb, I.Tews, and E.Schleiff (2008).
pH sensitivity of the GTPase Toc33 as a regulatory circuit for protein translocation into chloroplasts.
  Plant Cell Physiol, 49, 1917-1921.  
17465725 J.J.Yeh, and C.J.Der (2007).
Targeting signal transduction in pancreatic cancer treatment.
  Expert Opin Ther Targets, 11, 673-694.  
17261588 L.E.Reddick, M.D.Vaughn, S.J.Wright, I.M.Campbell, and B.D.Bruce (2007).
In vitro comparative kinetic analysis of the chloroplast Toc GTPases.
  J Biol Chem, 282, 11410-11426.  
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.  
16172677 H.Sigel, and R.Griesser (2005).
Nucleoside 5'-triphosphates: self-association, acid-base, and metal ion-binding properties in solution.
  Chem Soc Rev, 34, 875-900.  
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.  
14585972 M.J.Seewald, A.Kraemer, M.Farkasovsky, C.Körner, A.Wittinghofer, and I.R.Vetter (2003).
Biochemical characterization of the Ran-RanBP1-RanGAP system: are RanBP proteins and the acidic tail of RanGAP required for the Ran-RanGAP GTPase reaction?
  Mol Cell Biol, 23, 8124-8136.  
12397065 Y.T.Chou, J.F.Swain, and L.M.Gierasch (2002).
Functionally significant mobile regions of Escherichia coli SecA ATPase identified by NMR.
  J Biol Chem, 277, 50985-50990.  
11575773 H.Sigel, E.M.Bianchi, N.A.Corfù, Y.Kinjo, R.Tribolet, and R.B.Martin (2001).
Stabilities and isomeric equilibria in solutions of monomeric metal-ion complexes of guanosine 5'-triphosphate (GTP4-) and inosine 5'-triphosphate (ITP4-) in comparison with those of adenosine 5'-triphosphate (ATP4-).
  Chemistry, 7, 3729-3737.  
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.  
11188692 C.T.Farrar, J.Ma, D.J.Singel, and C.J.Halkides (2000).
Structural changes induced in p21Ras upon GAP-334 complexation as probed by ESEEM spectroscopy and molecular-dynamics simulation.
  Structure, 8, 1279-1287.  
  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.  
10194860 C.F.Huang, and N.N.Chuang (1999).
Facilitated geranylgeranylation of shrimp ras-encoded p25 fusion protein by the binding with guanosine diphosphate.
  J Exp Zool, 283, 510-521.  
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
9632652 W.P.Ciesla, and D.A.Bobak (1998).
Clostridium difficile toxins A and B are cation-dependent UDP-glucose hydrolases with differing catalytic activities.
  J Biol Chem, 273, 16021-16026.  
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 codes are shown on the right.