1XE7

Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly roll fold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold

Zhou, C.-Z.Meyer, P.Quevillon-Cheruel, S.Li De La Sierra-Gallay, I.Collinet, B.Graille, M.Blondeau, K.Leulliot, N.Sorel, I.Poupon, A.Janin, J.Van Tilbeurgh, H.

(2005) Protein Sci 14: 209-215

  • DOI: 10.1110/ps.041121305
  • Primary Citation of Related Structures:  
    1XE8, 1XE7

  • PubMed Abstract: 
  • We determined the three-dimensional crystal structure of the protein YML079wp, encoded by a hypothetical open reading frame from Saccharomyces cerevisiae to a resolution of 1.75 A. The protein has no close homologs and its molecular and cellular functions are unknown ...

    We determined the three-dimensional crystal structure of the protein YML079wp, encoded by a hypothetical open reading frame from Saccharomyces cerevisiae to a resolution of 1.75 A. The protein has no close homologs and its molecular and cellular functions are unknown. The structure of the protein is a jelly-roll fold consisting of ten beta-strands organized in two parallel packed beta-sheets. The protein has strong structural resemblance to the plant storage and ligand binding proteins (canavalin, glycinin, auxin binding protein) but also to some plant and bacterial enzymes (epimerase, germin). The protein forms homodimers in the crystal, confirming measurements of its molecular mass in solution. Two monomers have their beta-sheet packed together to form the dimer. The presence of a hydrophobic ligand in a well conserved pocket inside the barrel and local sequence similarity with bacterial epimerases may suggest a biochemical function for this protein.


    Organizational Affiliation

    Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, Centre National de la Recherche Scientifique-Unité Mixte de Recherche 8619, Université Paris-Sud, 91405 Orsay, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypothetical 22.5 kDa protein in TUB1-CPR3 intergenic regionA, B, C203Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YML079W
UniProt
Find proteins for Q03629 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03629 
Go to UniProtKB:  Q03629
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.8α = 90
b = 206.8β = 90
c = 206.8γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
XDSdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description