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4yfy

From Proteopedia

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X-ray structure of the Viof N-formyltransferase from Providencia alcalifaciens O30 in complex with THF and TDP-Qui4N

Structural highlights

4yfy is a 2 chain structure with sequence from Providencia alcalifaciens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4yfy"

@@ Line 1: / Line 1: @@
 ==X-ray structure of the Viof N-formyltransferase from Providencia alcalifaciens O30 in complex with THF and TDP-Qui4N==
-<StructureSection load='4yfy' size='340' side='right' caption='[[4yfy]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='4yfy' size='340' side='right'caption='[[4yfy]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4yfy]] is a 2 chain structure. 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yfv|4yfv]]</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='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://www.rcsb.org/pdb/explore.do?structureId=4yfy RCSB], [http://www.ebi.ac.uk/pdbsum/4yfy PDBsum]</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=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>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/M9P0Q2_9GAMM M9P0Q2_9GAMM]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 15: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4yfy" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Benning, M M]]
+[[Category: Large Structures]]
-[[Category: Genthe, N A]]
+[[Category: Providencia alcalifaciens]]
-[[Category: Holden, H M]]
+[[Category: Benning MM]]
-[[Category: Thoden, J B]]
+[[Category: Genthe NA]]
-[[Category: Lipopolysaccharide o-antigen]]
+[[Category: Holden HM]]
-[[Category: Transferase]]
+[[Category: Thoden JB]]

4yfy

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Current revision

X-ray structure of the Viof N-formyltransferase from Providencia alcalifaciens O30 in complex with THF and TDP-Qui4N

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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