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| | ==X-ray Structure of the E224Q mutant of TcaB9, a C-3'-Methyltransferase, in Complex with S-Adenosyl-L-Homocysteine and Sugar Product== | | ==X-ray Structure of the E224Q mutant of TcaB9, a C-3'-Methyltransferase, in Complex with S-Adenosyl-L-Homocysteine and Sugar Product== |
| - | <StructureSection load='4e2y' size='340' side='right' caption='[[4e2y]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='4e2y' size='340' side='right'caption='[[4e2y]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4e2y]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Micromonospora_chalcea Micromonospora chalcea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E2Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E2Y FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4e2y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Micromonospora_chalcea Micromonospora chalcea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E2Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E2Y FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=JHZ:(2R,4S,6R)-4-AMINO-4,6-DIMETHYL-5-OXOTETRAHYDRO-2H-PYRAN-2-YL+[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE+(NON-PREFERRED+NAME)'>JHZ</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.8Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4e2w|4e2w]], [[4e2x|4e2x]], [[4e2z|4e2z]], [[4e30|4e30]], [[4e31|4e31]], [[4e32|4e32]], [[4e33|4e33]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JHZ:(2R,4S,6R)-4-amino-4,6-dimethyl-5-oxotetrahydro-2H-pyran-2-yl+[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl+dihydrogen+diphosphate+(non-preferred+name)'>JHZ</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tcab9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1874 Micromonospora chalcea])</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=4e2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2y OCA], [https://pdbe.org/4e2y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e2y RCSB], [https://www.ebi.ac.uk/pdbsum/4e2y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2y 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=4e2y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e2y RCSB], [http://www.ebi.ac.uk/pdbsum/4e2y PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/B5L6K6_MICCH B5L6K6_MICCH] |
| - | d-Tetronitrose is a nitro-containing tetradeoxysugar found attached to the antitumor and antibacterial agent tetrocarcin A. The biosynthesis of this highly unusual sugar in Micromonospora chalcea requires ten enzymes. The fifth step in the pathway involves the transfer of a methyl group from S-adenosyl-l-methionine (SAM) to the C-3' carbon of dTDP-3-amino-2,3,6-trideoxy-4-keto-d-glucose. The enzyme responsible for this transformation is referred to as TcaB9. It is a monomeric enzyme with a molecular architecture based around three domains. The N-terminal motif contains a binding site for a structural zinc ion. The middle- and C-terminal domains serve to anchor the SAM and dTDP-sugar ligands, respectively, to the protein, and the active site of TcaB9 is wedged between these two regions. For this investigation, the roles of Tyr 76, His 181, Tyr 222, Glu 224, and His 225, which form the active site of TcaB9, were probed by site-directed mutagenesis, kinetic analyses, and X-ray structural studies. In addition, two ternary complexes of the enzyme with bound S-adenosyl-l-homocysteine and either dTDP-3-amino-2,3,6-trideoxy-4-keto-d-glucose or dTDP-3-amino-2,3,6-trideoxy-d-galactose were determined to 1.5-A or 1.6-A resolution, respectively. Taken together, these investigations highlight the important role of His 225 in methyl transfer. In addition, the structural data suggest that the methylation reaction occurs via retention of configuration about the C-3' carbon of the sugar.
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| - | Probing the catalytic mechanism of a C-3'-methyltransferase involved in the biosynthesis of D-tetronitrose.,Bruender NA, Holden HM Protein Sci. 2012 Apr 11. doi: 10.1002/pro.2074. PMID:22495991<ref>PMID:22495991</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Micromonospora chalcea]] | | [[Category: Micromonospora chalcea]] |
| - | [[Category: Bruender, N A]] | + | [[Category: Bruender NA]] |
| - | [[Category: Holden, H M]] | + | [[Category: Holden HM]] |
| - | [[Category: Keto sugar]]
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| - | [[Category: Kijanose]]
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| - | [[Category: Sugar methylation]]
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| - | [[Category: Tetradeoxy sugar]]
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| - | [[Category: Tetronitrose]]
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| - | [[Category: Transferase]]
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