3frk: Difference between revisions
From Proteopedia
Jump to navigationJump to search
m Protected "3frk" [edit=sysop:move=sysop] |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image: | ==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=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3frk]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FRK FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">qdtB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1517 Thermoanaerobacterium thermosaccharolyticum])</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=3frk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3frk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3frk RCSB], [http://www.ebi.ac.uk/pdbsum/3frk PDBsum]</span></td></tr> | |||
</table> | |||
== 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/chain_selection.php?pdb_ID=2ata 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> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Thermoanaerobacterium thermosaccharolyticum]] | [[Category: Thermoanaerobacterium thermosaccharolyticum]] | ||
[[Category: Holden, H M | [[Category: Holden, H M]] | ||
[[Category: Thoden, J B | [[Category: Thoden, J B]] | ||
[[Category: Aminotransferase]] | [[Category: Aminotransferase]] | ||
[[Category: Natural porduct]] | [[Category: Natural porduct]] | ||
[[Category: Sugar-modification]] | [[Category: Sugar-modification]] | ||
[[Category: Transferase]] | [[Category: Transferase]] | ||
Revision as of 10:17, 3 December 2014
X-ray structure of QdtB from T. thermosaccharolyticum in complex with a PLP:TDP-3-aminoquinovose aldimine
| ||||||||||||
