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3frk
From Proteopedia
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| - | {{Seed}} | ||
| - | [[Image:3frk.jpg|left|200px]] | ||
| - | < | + | ==X-ray structure of QdtB from T. thermosaccharolyticum in complex with a PLP:TDP-3-aminoquinovose aldimine== |
| - | + | <StructureSection load='3frk' size='340' side='right'caption='[[3frk]], [[Resolution|resolution]] 2.15Å' scene=''> | |
| - | You may | + | == Structural highlights == |
| - | or the | + | <table><tr><td colspan='2'>[[3frk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacterium_thermosaccharolyticum Thermoanaerobacterium thermosaccharolyticum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FRK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FRK FirstGlance]. <br> |
| - | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15Å</td></tr> | |
| - | -- | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TQP:(2R,3R,4S,5S,6R)-3,5-DIHYDROXY-4-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}-6-METHYLTETRAHYDRO-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'>TQP</scene></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=3frk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3frk OCA], [https://pdbe.org/3frk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3frk RCSB], [https://www.ebi.ac.uk/pdbsum/3frk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3frk ProSAT]</span></td></tr> | |
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q6TFC4_THETR Q6TFC4_THETR] | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fr/3frk_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3frk ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 3-Acetamido-3,6-dideoxy-alpha-d-glucose or Quip3NAc is an unusual deoxyamino sugar found in the O-antigens of some Gram-negative bacteria and in the S-layers of Gram-positive bacteria. It is synthesized in these organisms as a dTDP-linked sugar via the action of five enzymes. The focus of this investigation is on QdtB from Thermoanaerobacterium thermosaccharolyticum E207-71, a PLP-dependent aminotransferase that catalyzes the penultimate step in the production of dTDP-Quip3NAc. For this analysis, the enzyme was crystallized in the presence of its product, dTDP-Quip3N, and the structure was solved and refined to 2.15 A resolution. QdtB is a dimer, and its overall fold places it into the well-characterized aspartate aminotransferase superfamily. Electron density corresponding to the bound product reveals the presence of a Schiff base between C-4' of the PLP cofactor and the amino nitrogen of the sugar. Those amino acid side chains involved in binding the dTDP-sugar into the active site include Tyr 183, His 309, and Tyr 310 from subunit 1 and Lys 219 from subunit 2. Notably there is a decided lack of interactions between the pyranosyl C-4' hydroxyl of the dTDP-sugar and the protein. In keeping with this observation, we show that QdtB can also turn over dTDP-3-acetamido-3,6-dideoxy-alpha-d-galactose. This investigation represents the first structural analysis of a sugar-modifying aminotransferase with a bound product in its active site that functions at the C-3' rather than the C-4' position of the hexose. | ||
| - | + | Structural analysis of QdtB, an aminotransferase required for the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-glucose.,Thoden JB, Schaffer C, Messner P, Holden HM Biochemistry. 2009 Feb 24;48(7):1553-61. PMID:19178182<ref>PMID:19178182</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | == | + | </div> |
| - | + | <div class="pdbe-citations 3frk" style="background-color:#fffaf0;"></div> | |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Thermoanaerobacterium thermosaccharolyticum]] | [[Category: Thermoanaerobacterium thermosaccharolyticum]] | ||
| - | [[Category: Holden | + | [[Category: Holden HM]] |
| - | [[Category: Thoden | + | [[Category: Thoden JB]] |
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Current revision
X-ray structure of QdtB from T. thermosaccharolyticum in complex with a PLP:TDP-3-aminoquinovose aldimine
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