4mzu: Difference between revisions

Line 1:

~~{{STRUCTURE_4mzu| PDB=4mzu | SCENE= }}~~

==Crystal structure of FdtD, a bifunctional ketoisomerase/N-acetyltransferase from Shewanella denitrificans==

===Crystal structure of FdtD, a bifunctional ketoisomerase/N-acetyltransferase from Shewanella denitrificans===

~~{{ABSTRACT_PUBMED_24128043}}~~

== Structural highlights ==

<table><tr><td colspan='2'>[[4mzu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Shedo Shedo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MZU FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>

<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">FdtD, Sden_2659 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318161 SHEDO])</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=4mzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mzu RCSB], [http://www.ebi.ac.uk/pdbsum/4mzu PDBsum]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Unusual N-acetylated sugars have been observed on the O-antigens of some Gram-negative bacteria and on the S-layers of both Gram-positive and Gram-negative bacteria. One such sugar is 3-acetamido-3,6-dideoxy-alpha-d-galactose or Fuc3NAc. The pathway for its production requires five enzymes with the first step involving the attachment of dTMP to glucose-1-phosphate. Here, we report a structural and biochemical characterization of a bifunctional enzyme from Shewanella denitificans thought to be involved in the biosynthesis of dTDP-Fuc3NAc. On the basis of a bioinformatics analysis, the enzyme, hereafter referred to as FdtD, has been postulated to catalyze the third and fifth steps in the pathway, namely, a 3,4-keto isomerization and an N-acetyltransferase reaction. For the X-ray analysis reported here, the enzyme was crystallized in the presence of dTDP and CoA. The crystal structure shows that FdtD adopts a hexameric quaternary structure with 322 symmetry. Each subunit of the hexamer folds into two distinct domains connected by a flexible loop. The N-terminal domain adopts a left-handed beta-helix motif and is responsible for the N-acetylation reaction. The C-terminal domain folds into an antiparallel flattened beta-barrel that harbors the active site responsible for the isomerization reaction. Biochemical assays verify the two proposed catalytic activities of the enzyme and reveal that the 3,4-keto isomerization event leads to the inversion of configuration about the hexose C-4' carbon.

~~==About this Structure==~~

Structural and Biochemical Characterization of a Bifunctional Ketoisomerase/N-Acetyltransferase from Shewanella denitrificans.,Chantigian DP, Thoden JB, Holden HM Biochemistry. 2013 Nov 19;52(46):8374-85. doi: 10.1021/bi401170t. Epub 2013 Nov, 4. PMID:24128043<ref>PMID:24128043</ref>

~~[[4mzu]] is~~ a ~~12 chain structure with sequence~~ from ~~[http://en~~.~~wikipedia~~.~~org/wiki/Shedo Shedo]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.~~ac.il/oca-bin~~/~~ocashort?id=4MZU OCA].~~

==~~Reference~~==

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

~~<ref group="xtra">PMID:024128043</ref>~~<references ~~group="xtra"~~/><~~references~~/>

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Shedo]]

[[Category: Chantigian, D P.]]

[[Category: Chantigian, D P]]

[[Category: Holden, H M.]]

[[Category: Holden, H M]]

[[Category: Thoden, J B.]]

[[Category: Thoden, J B]]

[[Category: Acetyl-coenzyme some]]

[[Category: Beta-helix]]

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@@ Line 1: / Line 1: @@
-{{STRUCTURE_4mzu|  PDB=4mzu  |  SCENE=  }}
+==Crystal structure of FdtD, a bifunctional ketoisomerase/N-acetyltransferase from Shewanella denitrificans==
-===Crystal structure of FdtD, a bifunctional ketoisomerase/N-acetyltransferase from Shewanella denitrificans===
+<StructureSection load='4mzu' size='340' side='right' caption='[[4mzu]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-{{ABSTRACT_PUBMED_24128043}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4mzu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Shedo Shedo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MZU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MZU FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TDR:THYMINE'>TDR</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">FdtD, Sden_2659 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318161 SHEDO])</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=4mzu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mzu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4mzu RCSB], [http://www.ebi.ac.uk/pdbsum/4mzu PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Unusual N-acetylated sugars have been observed on the O-antigens of some Gram-negative bacteria and on the S-layers of both Gram-positive and Gram-negative bacteria. One such sugar is 3-acetamido-3,6-dideoxy-alpha-d-galactose or Fuc3NAc. The pathway for its production requires five enzymes with the first step involving the attachment of dTMP to glucose-1-phosphate. Here, we report a structural and biochemical characterization of a bifunctional enzyme from Shewanella denitificans thought to be involved in the biosynthesis of dTDP-Fuc3NAc. On the basis of a bioinformatics analysis, the enzyme, hereafter referred to as FdtD, has been postulated to catalyze the third and fifth steps in the pathway, namely, a 3,4-keto isomerization and an N-acetyltransferase reaction. For the X-ray analysis reported here, the enzyme was crystallized in the presence of dTDP and CoA. The crystal structure shows that FdtD adopts a hexameric quaternary structure with 322 symmetry. Each subunit of the hexamer folds into two distinct domains connected by a flexible loop. The N-terminal domain adopts a left-handed beta-helix motif and is responsible for the N-acetylation reaction. The C-terminal domain folds into an antiparallel flattened beta-barrel that harbors the active site responsible for the isomerization reaction. Biochemical assays verify the two proposed catalytic activities of the enzyme and reveal that the 3,4-keto isomerization event leads to the inversion of configuration about the hexose C-4' carbon.
-==About this Structure==
+Structural and Biochemical Characterization of a Bifunctional Ketoisomerase/N-Acetyltransferase from Shewanella denitrificans.,Chantigian DP, Thoden JB, Holden HM Biochemistry. 2013 Nov 19;52(46):8374-85. doi: 10.1021/bi401170t. Epub 2013 Nov, 4. PMID:24128043<ref>PMID:24128043</ref>
-[[4mzu]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Shedo Shedo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MZU OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:024128043</ref><references group="xtra"/><references/>
+</div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Shedo]]
-[[Category: Chantigian, D P.]]
+[[Category: Chantigian, D P]]
-[[Category: Holden, H M.]]
+[[Category: Holden, H M]]
-[[Category: Thoden, J B.]]
+[[Category: Thoden, J B]]
 [[Category: Acetyl-coenzyme some]]
 [[Category: Beta-helix]]