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| | <StructureSection load='2idk' size='340' side='right'caption='[[2idk]], [[Resolution|resolution]] 2.55Å' scene=''> | | <StructureSection load='2idk' size='340' side='right'caption='[[2idk]], [[Resolution|resolution]] 2.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2idk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IDK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2idk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IDK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2F:5-METHYL-5,6,7,8-TETRAHYDROFOLIC+ACID'>C2F</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]] 2.55Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1bhj|1bhj]], [[1nbh|1nbh]], [[1nbi|1nbi]], [[1r74|1r74]], [[1r8x|1r8x]], [[2idj|2idj]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C2F:5-METHYL-5,6,7,8-TETRAHYDROFOLIC+ACID'>C2F</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GNMT ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glycine_N-methyltransferase Glycine N-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.20 2.1.1.20] </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=2idk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2idk OCA], [https://pdbe.org/2idk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2idk RCSB], [https://www.ebi.ac.uk/pdbsum/2idk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2idk ProSAT]</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=2idk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2idk OCA], [https://pdbe.org/2idk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2idk RCSB], [https://www.ebi.ac.uk/pdbsum/2idk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2idk ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/GNMT_RAT GNMT_RAT]] Catalyzes the methylation of glycine by using S-adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine) with the concomitant production of S-adenosylhomocysteine (AdoHcy). Possible crucial role in the regulation of tissue concentration of AdoMet and of metabolism of methionine.
| + | [https://www.uniprot.org/uniprot/GNMT_RAT GNMT_RAT] Catalyzes the methylation of glycine by using S-adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine) with the concomitant production of S-adenosylhomocysteine (AdoHcy). Possible crucial role in the regulation of tissue concentration of AdoMet and of metabolism of methionine. |
| | == 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: Buffalo rat]] | |
| - | [[Category: Glycine N-methyltransferase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Egli, M]] | + | [[Category: Rattus norvegicus]] |
| - | [[Category: Loukachevitch, L V]] | + | [[Category: Egli M]] |
| - | [[Category: Luka, Z]] | + | [[Category: Loukachevitch LV]] |
| - | [[Category: Newcomer, M E]] | + | [[Category: Luka Z]] |
| - | [[Category: Pakhomova, S]] | + | [[Category: Newcomer ME]] |
| - | [[Category: Wagner, C]] | + | [[Category: Pakhomova S]] |
| - | [[Category: Folate binding]]
| + | [[Category: Wagner C]] |
| - | [[Category: Glycine n-methyltransferase]]
| + | |
| - | [[Category: Rat]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
GNMT_RAT Catalyzes the methylation of glycine by using S-adenosylmethionine (AdoMet) to form N-methylglycine (sarcosine) with the concomitant production of S-adenosylhomocysteine (AdoHcy). Possible crucial role in the regulation of tissue concentration of AdoMet and of metabolism of methionine.
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
Glycine N-methyltransferase (GNMT) is a key regulatory enzyme in methyl group metabolism. It is abundant in the liver, where it uses excess S-adenosylmethionine (AdoMet) to methylate glycine to N-methylglycine (sarcosine) and produces S-adenosylhomocysteine (AdoHcy), thereby controlling the methylating potential of the cell. GNMT also links utilization of preformed methyl groups, in the form of methionine, to their de novo synthesis, because it is inhibited by a specific form of folate, 5-methyltetrahydrofolate. Although the structure of the enzyme has been elucidated by x-ray crystallography of the apoenzyme and in the presence of the substrate, the location of the folate inhibitor in the tetrameric structure has not been identified. We report here for the first time the crystal structure of rat GNMT complexed with 5-methyltetrahydrofolate. In the GNMT-folate complex, two folate binding sites were located in the intersubunit areas of the tetramer. Each folate binding site is formed primarily by two 1-7 N-terminal regions of one pair of subunits and two 205-218 regions of the other pair of subunits. Both the pteridine and p-aminobenzoyl rings are located in the hydrophobic cavities formed by Tyr5, Leu207, and Met215 residues of all subunits. Binding experiments in solution also confirm that one GNMT tetramer binds two folate molecules. For the enzymatic reaction to take place, the N-terminal fragments of GNMT must have a significant degree of conformational freedom to provide access to the active sites. The presence of the folate in this position provides a mechanism for its inhibition.
5-methyltetrahydrofolate is bound in intersubunit areas of rat liver folate-binding protein glycine N-methyltransferase.,Luka Z, Pakhomova S, Loukachevitch LV, Egli M, Newcomer ME, Wagner C J Biol Chem. 2007 Feb 9;282(6):4069-75. Epub 2006 Dec 7. PMID:17158459[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Luka Z, Pakhomova S, Loukachevitch LV, Egli M, Newcomer ME, Wagner C. 5-methyltetrahydrofolate is bound in intersubunit areas of rat liver folate-binding protein glycine N-methyltransferase. J Biol Chem. 2007 Feb 9;282(6):4069-75. Epub 2006 Dec 7. PMID:17158459 doi:10.1074/jbc.M610384200
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