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 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
A, E, I, M
211Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRI1
EC: 5.3.1.23
Find proteins for Q06489 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRI1
Go to UniProtKB:  Q06489
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
B, F, J, N
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MRI1
EC: 5.3.1.23
Find proteins for Q06489 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MRI1
Go to UniProtKB:  Q06489
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, E, I, M
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, E, F, I, J, M, N
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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.620α = 90.00
b = 105.450β = 90.00
c = 263.050γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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