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| | ==Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), complexes with reaction intermediates== | | ==Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), complexes with reaction intermediates== |
| - | <StructureSection load='6cd1' size='340' side='right' caption='[[6cd1]], [[Resolution|resolution]] 1.91Å' scene=''> | + | <StructureSection load='6cd1' size='340' side='right'caption='[[6cd1]], [[Resolution|resolution]] 1.91Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6cd1]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Barrel_medic Barrel medic]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CD1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6cd1]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Medicago_truncatula Medicago truncatula]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CD1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PLS:[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE'>PLS</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]] 1.91Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=PLG:N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]'>PLG</scene>, <scene name='pdbligand=PLS:[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE'>PLS</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">11445860, MTR_2g018290 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3880 Barrel medic])</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=6cd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cd1 OCA], [https://pdbe.org/6cd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cd1 RCSB], [https://www.ebi.ac.uk/pdbsum/6cd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cd1 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </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=6cd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cd1 OCA], [http://pdbe.org/6cd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cd1 RCSB], [http://www.ebi.ac.uk/pdbsum/6cd1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cd1 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/G7ILW0_MEDTR G7ILW0_MEDTR]] Interconversion of serine and glycine.[RuleBase:RU000585] | + | [https://www.uniprot.org/uniprot/G7ILW0_MEDTR G7ILW0_MEDTR] Interconversion of serine and glycine.[RuleBase:RU000585] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6cd1" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6cd1" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Serine hydroxymethyltransferase 3D structures|Serine hydroxymethyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Barrel medic]] | + | [[Category: Large Structures]] |
| - | [[Category: Glycine hydroxymethyltransferase]] | + | [[Category: Medicago truncatula]] |
| - | [[Category: Dauter, Z]] | + | [[Category: Dauter Z]] |
| - | [[Category: Ruszkowska, A]] | + | [[Category: Ruszkowska A]] |
| - | [[Category: Ruszkowski, M]] | + | [[Category: Ruszkowski M]] |
| - | [[Category: Sekula, B]] | + | [[Category: Sekula B]] |
| - | [[Category: Chloroplast]]
| + | |
| - | [[Category: One-carbon cycle]]
| + | |
| - | [[Category: Plp]]
| + | |
| - | [[Category: Plp-glycine]]
| + | |
| - | [[Category: Plp-serine]]
| + | |
| - | [[Category: Tetrahydrofolate]]
| + | |
| - | [[Category: Tetramer]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
6cd1 is a 8 chain structure with sequence from Medicago truncatula. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.91Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
G7ILW0_MEDTR Interconversion of serine and glycine.[RuleBase:RU000585]
Publication Abstract from PubMed
Serine hydroxymethyltransferase (SHMT, EC 2.1.2.1) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme which catalyzes the reversible serine-to-glycine conversion in either a tetrahydrofolate-dependent or -independent manner. The enzyme is also responsible for the tetrahydrofolate-independent cleavage of other beta-hydroxy amino acids. In addition to being an essential player in the serine homeostasis, SHMT action is the main source of activated one-carbon units, which links SHMT activity with the control of cell proliferation. In plants, studies of SHMT enzymes are more complicated than of those of, e.g., bacterial or mammalian origins because plant genomes encode multiple SHMT isozymes that are targeted to different subcellular compartments: cytosol, mitochondria, plastids, and nucleus. Here we report crystal structures of chloroplast-targeted SHMT from Medicago truncatula (MtSHMT3). MtSHMT3 is a tetramer in solution, composed of two tight and obligate dimers. Our complexes with PLP internal aldimine, PLP-serine and PLP-glycine external aldimines, and PLP internal aldimine with a free glycine reveal structural details of the MtSHMT3-catalyzed reaction. Capturing the enzyme in different stages along the course of the slow tetrahydrofolate-independent serine-to-glycine conversion allowed to observe a unique conformation of the PLP-serine gamma-hydroxyl group, and a concerted movement of two tyrosine residues in the active site.
Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization.,Ruszkowski M, Sekula B, Ruszkowska A, Dauter Z Front Plant Sci. 2018 May 11;9:584. doi: 10.3389/fpls.2018.00584. eCollection, 2018. PMID:29868052[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ruszkowski M, Sekula B, Ruszkowska A, Dauter Z. Chloroplastic Serine Hydroxymethyltransferase From Medicago truncatula: A Structural Characterization. Front Plant Sci. 2018 May 11;9:584. doi: 10.3389/fpls.2018.00584. eCollection, 2018. PMID:29868052 doi:http://dx.doi.org/10.3389/fpls.2018.00584
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