1C03

CRYSTAL STRUCTURE OF YPD1P (TRICLINIC FORM)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Insights into eukaryotic multistep phosphorelay signal transduction revealed by the crystal structure of Ypd1p from Saccharomyces cerevisiae.

Song, H.K., Lee, J.Y., Lee, M.G., Moon, J., Min, K., Yang, J.K., Suh, S.W.

(1999) J Mol Biol 293: 753-761

  • DOI: 10.1006/jmbi.1999.3215
  • Primary Citation of Related Structures:  
    1C02, 1C03

  • PubMed Abstract: 

    • "Two-component" phosphorelay signal transduction systems constitute a potential target for antibacterial and antifungal agents, since they are found exclusively in prokaryotes and lower eukaryotes (yeast, fungi, slime mold, and plants) but not in mammalian organisms ...

    "Two-component" phosphorelay signal transduction systems constitute a potential target for antibacterial and antifungal agents, since they are found exclusively in prokaryotes and lower eukaryotes (yeast, fungi, slime mold, and plants) but not in mammalian organisms. Saccharomyces cerevisiae Ypd1p, a key intermediate in the osmosensing multistep phosphorelay signal transduction, catalyzes the phosphoryl group transfer between response regulators. Its 1.8 A structure, representing the first example of a eukaryotic phosphorelay protein, contains a four-helix bundle as in the HPt domain of Escherichia coli ArcB sensor kinase. However, Ypd1p has a 44-residue insertion between the last two helices of the helix bundle. The side-chain of His64, the site of phosphorylation, protrudes into the solvent. The structural resemblance between Ypd1p and ArcB HPt domain suggests that both prokaryotes and lower eukaryotes utilize the same basic protein fold for phosphorelay signal transduction. This study sheds light on the best characterized eukaryotic phosphorelay system.

    Related Citations: 
    • Crystallization and preliminary X-ray analysis of Saccharomyces cerevisiae Ypd1p, a key intermediate in phosphorelay signal transduction
      Lee, M.G., Lee, J.Y., Song, H.K., Suh, S.W.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 1219
    Organizational Affiliation: 

    Department of Chemistry College of Natural Sciences, Seoul National University, Seoul, 151-742, Korea.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYPOTHETICAL PROTEIN YDL235CA, B, C, D168Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q07688 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07688 
Go to UniProtKB:  Q07688
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07688
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.343α = 106.37
b = 66.48β = 106.66
c = 66.491γ = 115.33
Software Package:
Software NamePurpose
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-15
    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: 2017-02-01
    Changes: Structure summary
  • Version 1.4: 2017-02-08
    Changes: Database references
  • Version 1.5: 2021-07-07
    Changes: Refinement description