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| | ==Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits== | | ==Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits== |
| - | <StructureSection load='1w2w' size='340' side='right' caption='[[1w2w]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='1w2w' size='340' side='right'caption='[[1w2w]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1w2w]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W2W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W2W FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1w2w]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W2W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W2W FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1w2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w2w OCA], [https://pdbe.org/1w2w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w2w RCSB], [https://www.ebi.ac.uk/pdbsum/1w2w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w2w ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1w2w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w2w OCA], [http://pdbe.org/1w2w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w2w RCSB], [http://www.ebi.ac.uk/pdbsum/1w2w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1w2w ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/MTNA_YEAST MTNA_YEAST]] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).[HAMAP-Rule:MF_03119]<ref>PMID:15215245</ref> <ref>PMID:18625006</ref> | + | [https://www.uniprot.org/uniprot/MTNA_YEAST MTNA_YEAST] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).[HAMAP-Rule:MF_03119]<ref>PMID:15215245</ref> <ref>PMID:18625006</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | + | [[Category: Large Structures]] |
| - | [[Category: S-methyl-5-thioribose-1-phosphate isomerase]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Altmann, M]] | + | [[Category: Altmann M]] |
| - | [[Category: Baumann, U]] | + | [[Category: Baumann U]] |
| - | [[Category: Bigler, P]] | + | [[Category: Bigler P]] |
| - | [[Category: Bumann, M]] | + | [[Category: Bumann M]] |
| - | [[Category: Djafarzadeh, S]] | + | [[Category: Djafarzadeh S]] |
| - | [[Category: Oberholzer, A E]] | + | [[Category: Oberholzer AE]] |
| - | [[Category: Trachsel, H]] | + | [[Category: Trachsel H]] |
| - | [[Category: Eif2b]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Methionine salvage pathway]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Translation initiation]]
| + | |
| Structural highlights
Function
MTNA_YEAST Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).[HAMAP-Rule:MF_03119][1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits.,Bumann M, Djafarzadeh S, Oberholzer AE, Bigler P, Altmann M, Trachsel H, Baumann U J Biol Chem. 2004 Aug 27;279(35):37087-94. Epub 2004 Jun 23. PMID:15215245[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bumann M, Djafarzadeh S, Oberholzer AE, Bigler P, Altmann M, Trachsel H, Baumann U. Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits. J Biol Chem. 2004 Aug 27;279(35):37087-94. Epub 2004 Jun 23. PMID:15215245 doi:10.1074/jbc.M404458200
- ↑ Pirkov I, Norbeck J, Gustafsson L, Albers E. A complete inventory of all enzymes in the eukaryotic methionine salvage pathway. FEBS J. 2008 Aug;275(16):4111-20. doi: 10.1111/j.1742-4658.2008.06552.x. Epub, 2008 Jul 10. PMID:18625006 doi:10.1111/j.1742-4658.2008.06552.x
- ↑ Bumann M, Djafarzadeh S, Oberholzer AE, Bigler P, Altmann M, Trachsel H, Baumann U. Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits. J Biol Chem. 2004 Aug 27;279(35):37087-94. Epub 2004 Jun 23. PMID:15215245 doi:10.1074/jbc.M404458200
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