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PDBsum entry 1plk

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protein ligands metals links
Oncogene protein PDB id
1plk
Jmol
Contents
Protein chain
141 a.a. *
Ligands
GTP
Metals
_MG
* Residue conservation analysis
PDB id:
1plk
Name: Oncogene protein
Title: Crystallographic studies on p21h-ras using synchrotron laue method: improvement of crystal quality and monitoring of the gtpase reaction at different time points
Structure: C-h-ras p21 protein. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.228    
Authors: A.Scheidig,A.Sanchez-Llorente,A.Lautwein,E.F.Pai, J.E.T.Corrie,G.P.Reid,A.Wittinghofer,R.S.Goody
Key ref:
A.J.Scheidig et al. (1994). Crystallographic studies on p21(H-ras) using the synchrotron Laue method: improvement of crystal quality and monitoring of the GTPase reaction at different time points. Acta Crystallogr D Biol Crystallogr, 50, 512-520. PubMed id: 15299412 DOI: 10.1107/S090744499301443X
Date:
13-Mar-94     Release date:   31-Jul-94    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01112  (RASH_HUMAN) -  GTPase HRas
Seq:
Struc:
189 a.a.
141 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 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: 10.1107/S090744499301443X Acta Crystallogr D Biol Crystallogr 50:512-520 (1994)
PubMed id: 15299412  
 
 
Crystallographic studies on p21(H-ras) using the synchrotron Laue method: improvement of crystal quality and monitoring of the GTPase reaction at different time points.
A.J.Scheidig, A.Sanchez-Llorente, A.Lautwein, E.F.Pai, J.E.Corrie, G.P.Reid, A.Wittinghofer, R.S.Goody.
 
  ABSTRACT  
 
The parameters affecting the crystal quality of complexes between p21(H-ras) and caged GTP have been investigated. The use of pure diastereomers of caged GTP complexed to the more stable p21(G12P)' mutant of p21 and the addition of n-octyl-beta-D-glucopyranoside improved the reproducibility and decreased the mosaicity of the crystals significantly. Furthermore, the crystallization technique was changed from the batch method to the sitting-drop technique. With the availability of a larger yield of well ordered crystals, it was possible to extend the time-resolved crystallographic investigations on p21(H-ras). A structure of p21(G12P)':GTP could be obtained 2 min after photolytic removal of the cage group and led to the identification of a previously unidentified conformation for the so-called catalytically active loop L4. The refinement of five data sets collected within 2 min at different times (2-4, 11-13, 20-22, 30-32 and 90-92 min) after the initiation of the intrinsic GTPase reaction of the protein indicates that the synchrotron Laue method can be used to detect small structural changes and alternative conformations, but is presently limited in the analysis of larger rearrangements since these produce diffuse and broken electron density.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Structures of the four different cage groups used for caged GTP during the crystallographic studies on p21" ...... . CI: l-(2- nitrophenyl)ethyl-, the asterisk marks the asymmetric substi- tuted C atom of the cage group; caged (R,S)-GTP is a mixture of pure caged(R)-GTP and pure caged(S)-GTP (ratio ca 1:!) according to Cahn-Ingold-Prelog nomenclature; C2: 2- nitrobenzyl-; C3: bis(2-nitrophenyl)methyl-; C4: 2-oxo-2-(4- methoxyphenyl)ethyl-.
Figure 5.
Fig. 5. Final (2E,- F,.) electron-density map, in stereo, around the ?,-phosphate group of the Laue structure 2 min after initiation of the reaction including the residues Thr58 to Gln61 of the loop L4. The electron density is contoured at the level of 25% CUt Off.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1994, 50, 512-520) copyright 1994.  
  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.  
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
9342335 J.Ma, and M.Karplus (1997).
Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21.
  Proc Natl Acad Sci U S A, 94, 11905-11910.  
8968112 N.E.Chayen, T.J.Boggon, A.Cassetta, A.Deacon, T.Gleichmann, J.Habash, S.J.Harrop, J.R.Helliwell, Y.P.Nieh, M.R.Peterson, J.Raftery, E.H.Snell, A.Hädener, A.C.Niemann, D.P.Siddons, V.Stojanoff, A.W.Thompson, T.Ursby, and M.Wulff (1996).
Trends and challenges in experimental macromolecular crystallography.
  Q Rev Biophys, 29, 227-278.  
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.