Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: The submitted conformer models are the 10 structures with the lowest total energy 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Solution structure of the Ras binding domain of the protein kinase Byr2 from Schizosaccharomyces pombe.

Gronwald, W.Huber, F.Grunewald, P.Sporner, M.Wohlgemuth, S.Herrmann, C.Kalbitzer, H.R.

(2001) Structure 9: 1029-1041

  • DOI: https://doi.org/10.1016/s0969-2126(01)00671-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    After activation, small GTPases such as Ras transfer the incoming signal to effectors by specifically interacting with the binding domain of these proteins. Structural details of the binding domain of different effectors determine which pathway is predominantly activated. Byr2 from fission yeast is a functional homolog of Raf, which is the direct downstream target of Ras in mammalians that initiates a protein kinase cascade. The amino acid sequence of Byr2's Ras binding domain is only weakly related to that of Raf, and Byr2's three-dimensional structure is unknown. We have solved the 3D structure of the Ras binding domain of Byr2 (Byr2RBD) from Schizosaccharomyces pombe in solution. The structure consists of three alpha helices and a mixed five-stranded beta pleated sheet arranged in the topology betabetaalphabetabetaalphabetaalpha with the first seven canonic secondary structure elements forming a ubiquitin superfold. 15N-(1)H-TROSY-HSQC spectroscopy of the complex of Byr2RBD with Ras*Mg(2+)*GppNHp reveals that the first and second beta strands and the first alpha helix of Byr2 are mainly involved in the protein-protein interaction as observed in other Ras binding domains. Although the putative interaction site of H-Ras from human and Ras1 from S. pombe are identical in sequence, binding to Byr2 leads to small but significant differences in the NMR spectra, indicating a slightly different binding mode. The ubiquitin superfold appears to be the general structural motif for Ras binding domains even in cases with vanishing sequence identity. However, details of the 3D structure and the interacting interface are different, thereby determining the specifity of the recognition of Ras and Ras-related proteins.

  • Organizational Affiliation

    Institut für Biophysik und physikalische Biochemie, Universität Regensburg, Postfach, D-93040, Regensburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN KINASE BYR295Schizosaccharomyces pombeMutation(s): 0 
Gene Names: BYR2 (AMINO ACIDS 71 - 165)
EC: 2.7.1
Find proteins for P28829 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P28829 
Go to UniProtKB:  P28829
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28829
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: The submitted conformer models are the 10 structures with the lowest total energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-12-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection