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5krv

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1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex Arginine

Structural highlights

5krv is a 2 chain structure with sequence from Vibrio vulnificus CMCP6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DXR_VIBVU Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).

Publication Abstract from PubMed

Vibrio vulnificus, a gram-negative bacterium, is the leading cause of seafood-borne illnesses and mortality in the United States. Previous studies have identified metabolites 2-C-methylerythritol 4-phosphate (MEP) as being essential for V. vulnificus growth and function. It was shown that 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) is a critical enzyme in the viability of V. vulnificus, and many other bacteria, as it catalyzes the rearrangement of 1-deoxy-D-xylulose-5-phosphate (Dxp) to 2-C-methylerythritol 4-phosphate (MEP) within the MEP pathway, found in plants and bacteria. The MEP pathway produces the isoprenoids, isopentenyl diphosphate and dimethylallyl pyrophosphate. In this study, we produced and structurally characterized V. vulnificus Dxr. The enzyme forms a dimeric assembly and contains a metal ion in the active site. Protein produced in Escherichia coli co-purifies with Mg(2+) ions, however the Mg(2+) cations may be substituted with Mn(2+), as both of these metals may be utilized by Dxrs. These findings will provide a basis for the design of Dxr inhibitors that may find application as antimicrobial compounds.

Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus.,Ussin NK, Bagnell AM, Offermann LR, Abdulsalam R, Perdue ML, Magee P, Chruszcz M Biochim Biophys Acta Proteins Proteom. 2018 Dec;1866(12):1209-1215. doi:, 10.1016/j.bbapap.2018.09.008. Epub 2018 Sep 29. PMID:30278288^[1]

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

References

↑ Ussin NK, Bagnell AM, Offermann LR, Abdulsalam R, Perdue ML, Magee P, Chruszcz M. Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus. Biochim Biophys Acta Proteins Proteom. 2018 Dec;1866(12):1209-1215. doi:, 10.1016/j.bbapap.2018.09.008. Epub 2018 Sep 29. PMID:30278288 doi:http://dx.doi.org/10.1016/j.bbapap.2018.09.008

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5krv"

@@ Line 3: / Line 3: @@
 <StructureSection load='5krv' size='340' side='right'caption='[[5krv]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5krv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibvu Vibvu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KRV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KRV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5krv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus_CMCP6 Vibrio vulnificus CMCP6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KRV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KRV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SRT:S,R+MESO-TARTARIC+ACID'>SRT</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]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5kqo|5kqo]], [[5krr|5krr]], [[5kry|5kry]], [[5ks1|5ks1]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SRT:S,R+MESO-TARTARIC+ACID'>SRT</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dxr, VV1_1866 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216895 VIBVU])</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=5krv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5krv OCA], [https://pdbe.org/5krv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5krv RCSB], [https://www.ebi.ac.uk/pdbsum/5krv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5krv ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </span></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=5krv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5krv OCA], [http://pdbe.org/5krv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5krv RCSB], [http://www.ebi.ac.uk/pdbsum/5krv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5krv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DXR_VIBVU DXR_VIBVU]] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).
+[https://www.uniprot.org/uniprot/DXR_VIBVU DXR_VIBVU] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 21: @@
 ==See Also==
-*[[DXP reductoisomerase|DXP reductoisomerase]]
+*[[DXP reductoisomerase 3D Structures|DXP reductoisomerase 3D Structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
 [[Category: Large Structures]]
-[[Category: Vibvu]]
+[[Category: Vibrio vulnificus CMCP6]]
-[[Category: Abdulsalam, R W]]
+[[Category: Abdulsalam RW]]
-[[Category: Chruszcz, M]]
+[[Category: Chruszcz M]]
-[[Category: Magee, P]]
+[[Category: Magee P]]
-[[Category: Ussin, N]]
+[[Category: Ussin N]]
-[[Category: Dxr 1-deoxy-d-xylulose 5-phosphate reductoisomerase]]
-[[Category: Oxidoreductase]]

5krv

From Proteopedia

Current revision

1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus in complex Arginine

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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