1W2W

Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

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Literature

Crystal Structure of Yeast Ypr118W, a Methylthioribose-1-Phosphate Isomerase Related to Regulatory Eif2B Subunits

Bumann, M., Djafarzadeh, S., Oberholzer, A.E., Bigler, P., Altmann, M., Trachsel, H., Baumann, U.

(2004) J Biol Chem 279: 37087

  • DOI: 10.1074/jbc.M404458200
  • Primary Citation of Related Structures:  
    1W2W

  • PubMed Abstract: 

    • Ypr118w is a non-essential, low copy number gene product from Saccharomyces cerevisiae. It belongs to the PFAM family PF01008, which contains the alpha-, beta-, and delta-subunits of eukaryotic translation initiation factor eIF2B, as well as proteins of unknown function from all three kingdoms ...

    Ypr118w is a non-essential, low copy number gene product from Saccharomyces cerevisiae. It belongs to the PFAM family PF01008, which contains the alpha-, beta-, and delta-subunits of eukaryotic translation initiation factor eIF2B, as well as proteins of unknown function from all three kingdoms. Recently, one of those latter proteins from Bacillus subtilis has been characterized as a 5-methylthioribose-1-phosphate isomerase, an enzyme of the methionine salvage pathway. We report here the crystal structure of Ypr118w, which reveals a dimeric protein with two domains and a putative active site cleft. The C-terminal domain resembles ribose-5-phosphate isomerase from Escherichia coli with a similar location of the active site. In vivo, Ypr118w protein is required for yeast cells to grow on methylthioadenosine in the absence of methionine, showing that Ypr118w is involved in the methionine salvage pathway. The crystal structure of Ypr118w reveals for the first time the fold of a PF01008 member and allows a deeper discussion of an enzyme of the methionine salvage pathway, which has in the past attracted interest due to tumor suppression and as a target of aniprotozoal drugs.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, Berne CH-3012.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASEA,
C [auth E],
E [auth I],
G [auth M]		211Saccharomyces cerevisiaeMutation(s): 0 
EC: 5.3.1.23
UniProt
Find proteins for Q06489 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06489 
Go to UniProtKB:  Q06489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06489
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASEB,
D [auth F],
F [auth J],
H [auth N]		191Saccharomyces cerevisiaeMutation(s): 0 
EC: 5.3.1.23
UniProt
Find proteins for Q06489 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06489 
Go to UniProtKB:  Q06489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06489
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A,
C [auth E],
E [auth I],
G [auth M]		L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.62α = 90
b = 105.45β = 90
c = 263.05γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other