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| | <StructureSection load='4yfy' size='340' side='right'caption='[[4yfy]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='4yfy' size='340' side='right'caption='[[4yfy]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4yfy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_inconstans"_ornstein_1920 "bacillus inconstans" ornstein 1920]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YFY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4yfy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Providencia_alcalifaciens Providencia alcalifaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YFY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0FX:DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE'>0FX</scene>, <scene name='pdbligand=1YJ:N-[4-({[(6R)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC+ACID'>1YJ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0FX:DTDP-4-AMINO-4,6-DIDEOXYGLUCOSE'>0FX</scene>, <scene name='pdbligand=1YJ:N-[4-({[(6R)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC+ACID'>1YJ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yfv|4yfv]]</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=4yfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfy OCA], [https://pdbe.org/4yfy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yfy RCSB], [https://www.ebi.ac.uk/pdbsum/4yfy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfy ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vioF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=126385 "Bacillus inconstans" Ornstein 1920])</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=4yfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfy OCA], [http://pdbe.org/4yfy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yfy RCSB], [http://www.ebi.ac.uk/pdbsum/4yfy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfy ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/M9P0Q2_9GAMM M9P0Q2_9GAMM] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus inconstans ornstein 1920]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Benning, M M]] | + | [[Category: Providencia alcalifaciens]] |
| - | [[Category: Genthe, N A]] | + | [[Category: Benning MM]] |
| - | [[Category: Holden, H M]] | + | [[Category: Genthe NA]] |
| - | [[Category: Thoden, J B]] | + | [[Category: Holden HM]] |
| - | [[Category: Lipopolysaccharide o-antigen]] | + | [[Category: Thoden JB]] |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
M9P0Q2_9GAMM
Publication Abstract from PubMed
The existence of N-formylated sugars in the O-antigens of Gram-negative bacteria has been known since the middle 1980s, but only recently have the biosynthetic pathways for their production been reported. In these pathways, glucose-1-phosphate is first activated by attachment to a dTMP moiety. This step is followed by a dehydration reaction and an amination. The last step in these pathways is catalyzed by N-formyltransferases that utilize N10 -formyltetrahydrofolate as the carbon source. Here we describe the three-dimensional structure of one of these N-formyltransferases, namely VioF from Providencia alcalifaciens O30. Specifically, this enzyme catalyzes the conversion of dTDP-4-amino-6-deoxyglucose (dTDP-Qui4N) to dTDP-4,6-dideoxy-4-formamido-d-glucose (dTDP-Qui4NFo). For this analysis, the structure of VioF was solved to 1.9 A resolution in both its apoform and in complex with tetrahydrofolate and dTDP-Qui4N. The crystals used in the investigation belonged to the space group R32 and demonstrated reticular merohedral twinning. The overall catalytic core of the VioF subunit is characterized by a six stranded mixed beta-sheet flanked on one side by three alpha-helices and on the other side by mostly random coil. This N-terminal domain is followed by an alpha-helix and a beta-hairpin that form the subunit:subunit interface. The active site of the enzyme is shallow and solvent-exposed. Notably, the pyranosyl moiety of dTDP-Qui4N is positioned into the active site by only one hydrogen bond provided by Lys 77. Comparison of the VioF model to that of a previously determined N-formyltransferase suggests that substrate specificity is determined by interactions between the protein and the pyrophosphoryl group of the dTDP-sugar substrate. This article is protected by copyright. All rights reserved.
Molecular Structure of an N-formyltransferase from Providencia alcalifaciens O30.,Genthe NA, Thoden JB, Benning MM, Holden HM Protein Sci. 2015 Mar 9. doi: 10.1002/pro.2675. PMID:25752909[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Genthe NA, Thoden JB, Benning MM, Holden HM. Molecular Structure of an N-formyltransferase from Providencia alcalifaciens O30. Protein Sci. 2015 Mar 9. doi: 10.1002/pro.2675. PMID:25752909 doi:http://dx.doi.org/10.1002/pro.2675
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