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4nak

From Proteopedia

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Arabidopsis thaliana IspD in complex with pentabromo-pseudilin

Structural highlights

4nak is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ISPD_ARATH Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). Is essential for chloroplast development and required for pigments and gibberellins biosynthesis.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The enzymes of the non-mevalonate pathway for isoprenoid biosynthesis have been identified as attractive targets with novel modes of action for the development of herbicides for crop protection and agents against infectious diseases. This pathway is present in many pathogenic organisms and plants, but absent in mammals. By using high-throughput screening, we identified highly halogenated marine natural products, the pseudilins, to be inhibitors of the third enzyme, IspD, in the pathway. Their activity against the IspD enzymes from Arabidopsis thaliana and Plasmodium vivax was determined in photometric and NMR-based assays. Cocrystal structures revealed that pseudilins bind to an allosteric pocket by using both divalent metal ion coordination and halogen bonding. The allosteric mode of action for preventing cosubstrate (CTP) binding at the active site was elucidated. Pseudilins show herbicidal activity in plant assays and antiplasmodial activity in cell-based assays.

Pseudilins: Halogenated, Allosteric Inhibitors of the Non-Mevalonate Pathway Enzyme IspD.,Kunfermann A, Witschel M, Illarionov B, Martin R, Rottmann M, Hoffken HW, Seet M, Eisenreich W, Knolker HJ, Fischer M, Bacher A, Groll M, Diederich F Angew Chem Int Ed Engl. 2014 Jan 20. doi: 10.1002/anie.201309557. PMID:24446431^[4]

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

References

↑ Rohdich F, Wungsintaweekul J, Eisenreich W, Richter G, Schuhr CA, Hecht S, Zenk MH, Bacher A. Biosynthesis of terpenoids: 4-diphosphocytidyl-2C-methyl-D-erythritol synthase of Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6451-6. PMID:10841550
↑ Okada K, Kawaide H, Kuzuyama T, Seto H, Curtis IS, Kamiya Y. Antisense and chemical suppression of the nonmevalonate pathway affects ent-kaurene biosynthesis in Arabidopsis. Planta. 2002 Jun;215(2):339-44. Epub 2002 Apr 12. PMID:12029484 doi:http://dx.doi.org/10.1007/s00425-002-0762-0
↑ Hsieh MH, Chang CY, Hsu SJ, Chen JJ. Chloroplast localization of methylerythritol 4-phosphate pathway enzymes and regulation of mitochondrial genes in ispD and ispE albino mutants in Arabidopsis. Plant Mol Biol. 2008 Apr;66(6):663-73. doi: 10.1007/s11103-008-9297-5. Epub 2008 , Jan 31. PMID:18236010 doi:http://dx.doi.org/10.1007/s11103-008-9297-5
↑ Kunfermann A, Witschel M, Illarionov B, Martin R, Rottmann M, Hoffken HW, Seet M, Eisenreich W, Knolker HJ, Fischer M, Bacher A, Groll M, Diederich F. Pseudilins: Halogenated, Allosteric Inhibitors of the Non-Mevalonate Pathway Enzyme IspD. Angew Chem Int Ed Engl. 2014 Jan 20. doi: 10.1002/anie.201309557. PMID:24446431 doi:http://dx.doi.org/10.1002/anie.201309557

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/4nak"

@@ Line 1: / Line 1: @@
 ==Arabidopsis thaliana IspD in complex with pentabromo-pseudilin==
-<StructureSection load='4nak' size='340' side='right' caption='[[4nak]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='4nak' size='340' side='right'caption='[[4nak]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4nak]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NAK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4nak]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NAK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PBQ:PENTABROMOPSEUDILIN'>PBQ</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]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1w77|1w77]], [[2yc5|2yc5]], [[1ini|1ini]], [[4nai|4nai]], [[4nal|4nal]], [[4nan|4nan]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PBQ:PENTABROMOPSEUDILIN'>PBQ</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At2g02500, ISPD, MCT, MECT, MEPCT, T8K22.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=4nak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nak OCA], [https://pdbe.org/4nak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nak RCSB], [https://www.ebi.ac.uk/pdbsum/4nak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nak 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/2-C-methyl-D-erythritol_4-phosphate_cytidylyltransferase 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.60 2.7.7.60] </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=4nak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nak OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nak RCSB], [http://www.ebi.ac.uk/pdbsum/4nak PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ISPD_ARATH ISPD_ARATH]] Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). Is essential for chloroplast development and required for pigments and gibberellins biosynthesis.<ref>PMID:10841550</ref> <ref>PMID:12029484</ref> <ref>PMID:18236010</ref>
+[https://www.uniprot.org/uniprot/ISPD_ARATH ISPD_ARATH] Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). Is essential for chloroplast development and required for pigments and gibberellins biosynthesis.<ref>PMID:10841550</ref> <ref>PMID:12029484</ref> <ref>PMID:18236010</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4nak" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[MEP cytidylyltransferase|MEP cytidylyltransferase]]
+*[[MEP cytidylyltransferase 3D structures|MEP cytidylyltransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Arath]]
+[[Category: Large Structures]]
-[[Category: Bacher, A]]
+[[Category: Bacher A]]
-[[Category: Diederich, F]]
+[[Category: Diederich F]]
-[[Category: Eisenreich, W]]
+[[Category: Eisenreich W]]
-[[Category: Fischer, M]]
+[[Category: Fischer M]]
-[[Category: Groll, M]]
+[[Category: Groll M]]
-[[Category: Hoffken, H W]]
+[[Category: Hoffken HW]]
-[[Category: Illarionov, B]]
+[[Category: Illarionov B]]
-[[Category: Knolker, H J]]
+[[Category: Knolker H-J]]
-[[Category: Kunfermann, A]]
+[[Category: Kunfermann A]]
-[[Category: Martin, R]]
+[[Category: Martin R]]
-[[Category: Rottmann, M]]
+[[Category: Rottmann M]]
-[[Category: Seet, M]]
+[[Category: Seet M]]
-[[Category: Witschel, M]]
+[[Category: Witschel M]]
-[[Category: Allosteric inhibition]]
-[[Category: Anti-infective]]
-[[Category: Drug discovery]]
-[[Category: Herbicide]]
-[[Category: Natural product]]
-[[Category: Pseudilin]]
-[[Category: Rossmann fold]]
-[[Category: Transferase]]
-[[Category: Transferase-transferase inhibitor complex]]

4nak

From Proteopedia

Current revision

Arabidopsis thaliana IspD in complex with pentabromo-pseudilin

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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