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4zu4

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Revision as of 07:41, 18 May 2023

X-ray structure of the 3,4-ketoisomerase domain of FdtD from Shewanella denitrificans

Structural highlights

4zu4 is a 6 chain structure with sequence from Shewanella denitrificans OS217. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q12KT8_SHEDO

Publication Abstract from PubMed

3-Acetamido-3,6-dideoxy-d-galactose (Fuc3NAc) and 3-acetamido-3,6-dideoxy-d-glucose (Qui3NAc) are unusual sugars found on the lipopolysaccharides of Gram-negative bacteria and on the S-layers of Gram-positive bacteria. The 3,4-ketoisomerases, referred to as FdtA and QdtA, catalyze the third steps in the respective biosynthetic pathways for these sugars. Whereas both enzymes utilize the same substrate, the stereochemistries of their products are different. Specifically, the hydroxyl groups at the hexose C-4' positions assume the "galactose" and "glucose" configurations in the FdtA and QdtA products, respectively. In 2007 we reported the structure of the apoform of FdtA from Aneurinibacillus thermoaerophilus, which was followed in 2014 by the X-ray analysis of QdtA from Thermoanaerobacterium thermosaccharolyticum as a binary complex. Both of these enzymes belong to the cupin superfamily. Here we report a combined structural and enzymological study to explore the manner in which these enzymes control the stereochemistry of their products. Various site-directed mutant proteins of each enzyme were constructed, and their dTDP-sugar products were analyzed by NMR spectroscopy. In addition, the kinetic parameters for these protein variants were measured, and the structure of one, namely, the QdtA Y17R/R97H double mutant form, was determined to 2.3-A resolution. Finally, in an attempt to obtain a model of FdtA with a bound dTDP-linked sugar, the 3,4-ketoisomerase domain of a bifunctional enzyme from Shewanella denitrificans was cloned, purified, and crystallized in the presence of a dTDP-linked sugar analogue. Taken together, the results from this investigation demonstrate that it is possible to convert a "galacto" enzyme into a "gluco" enzyme and vice versa.

Bacterial Sugar 3,4-Ketoisomerases: Structural Insight into Product Stereochemistry.,Thoden JB, Vinogradov E, Gilbert M, Salinger AJ, Holden HM Biochemistry. 2015 Jul 13. PMID:26125548^[1]

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

References

↑ Thoden JB, Vinogradov E, Gilbert M, Salinger AJ, Holden HM. Bacterial Sugar 3,4-Ketoisomerases: Structural Insight into Product Stereochemistry. Biochemistry. 2015 Jul 13. PMID:26125548 doi:http://dx.doi.org/10.1021/acs.biochem.5b00541

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/4zu4"

@@ Line 3: / Line 3: @@
 <StructureSection load='4zu4' size='340' side='right'caption='[[4zu4]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4zu4]] is a 6 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=4ZU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZU4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4zu4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_denitrificans_OS217 Shewanella denitrificans OS217]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZU4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4TG:DTDP-4,6-DIDEOXY-4-FORMAMIDO-GLUCOSE'>4TG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4TG:DTDP-4,6-DIDEOXY-4-FORMAMIDO-GLUCOSE'>4TG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4zu5|4zu5]]</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=4zu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zu4 OCA], [https://pdbe.org/4zu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zu4 RCSB], [https://www.ebi.ac.uk/pdbsum/4zu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zu4 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">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=4zu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zu4 OCA], [http://pdbe.org/4zu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zu4 RCSB], [http://www.ebi.ac.uk/pdbsum/4zu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zu4 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q12KT8_SHEDO Q12KT8_SHEDO]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Shedo]]
+[[Category: Shewanella denitrificans OS217]]
-[[Category: Gilbert, M]]
+[[Category: Gilbert M]]
-[[Category: Holden, H M]]
+[[Category: Holden HM]]
-[[Category: Salinger, A J]]
+[[Category: Salinger AJ]]
-[[Category: Thoden, J B]]
+[[Category: Thoden JB]]
-[[Category: Vinogradov, E]]
+[[Category: Vinogradov E]]
-[[Category: Cupin]]
-[[Category: Isomerase]]
-[[Category: Ketoisomerase]]
-[[Category: Lipopolysaccharide]]

4zu4

From Proteopedia

Revision as of 07:41, 18 May 2023

X-ray structure of the 3,4-ketoisomerase domain of FdtD from Shewanella denitrificans

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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