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6dbz

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Revision as of 17:18, 20 November 2019

Crystal structure of Nudix 1 from Arabidopsis thaliana complexed with isopentenyl diphosphate

Structural highlights

6dbz is a 2 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	6dby
Gene:	NUDT1, NUDX1, At1g68760, F14K14.13 (ARATH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[NUDT1_ARATH] Mediates the hydrolysis of some nucleoside diphosphate derivatives. Its substrate specificity is unclear. In vitro, it can use NTP, dNTP, 8-oxo-GTP, 8-oxo-dGTP, dGTP, dATP, dTTP or dihydroneopterin triphosphate (DHNTP) as substrate. Has some NADH pyrophosphatase activity in vitro; however, such activity may not be relevant in vivo due to the high concentration of manganese used during the experiments. Plays an important role in protection against oxidative DNA and RNA damage by removing oxidatively damaged form of guanine.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Plant genomes encode isopentenyl phosphate kinases (IPKs) that reactivate isopentenyl phosphate (IP) via ATP-dependent phosphorylation, forming the primary metabolite isopentenyl diphosphate (IPP) used generally for isoprenoid/terpenoid biosynthesis. Therefore, the existence of IPKs in plants raises unanswered questions concerning the origin and regulatory roles of IP in plant terpenoid metabolism. Here, we provide genetic and biochemical evidence showing that IP forms during specific dephosphorylation of IPP catalysed by a subset of Nudix superfamily hydrolases. Increasing metabolically available IP by overexpression of a bacterial phosphomevalonate decarboxylase (MPD) in Nicotiana tabacum resulted in significant enhancement in both monoterpene and sesquiterpene production. These results indicate that perturbing IP metabolism results in measurable changes in terpene products derived from both the methylerythritol phosphate (MEP) and mevalonate (MVA) pathways. Moreover, the unpredicted peroxisomal localization of bacterial MPD led us to discover that the step catalysed by phosphomevalonate kinase (PMK) imposes a hidden constraint on flux through the classical MVA pathway. These complementary findings fundamentally alter conventional views of metabolic regulation of terpenoid metabolism in plants and provide new metabolic engineering targets for the production of high-value terpenes in plants.

Contribution of isopentenyl phosphate to plant terpenoid metabolism.,Henry LK, Thomas ST, Widhalm JR, Lynch JH, Davis TC, Kessler SA, Bohlmann J, Noel JP, Dudareva N Nat Plants. 2018 Sep;4(9):721-729. doi: 10.1038/s41477-018-0220-z. Epub 2018 Aug , 20. PMID:30127411^[4]

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

References

↑ Klaus SM, Wegkamp A, Sybesma W, Hugenholtz J, Gregory JF 3rd, Hanson AD. A nudix enzyme removes pyrophosphate from dihydroneopterin triphosphate in the folate synthesis pathway of bacteria and plants. J Biol Chem. 2005 Feb 18;280(7):5274-80. Epub 2004 Dec 16. PMID:15611104 doi:http://dx.doi.org/M413759200
↑ Ogawa T, Ueda Y, Yoshimura K, Shigeoka S. Comprehensive analysis of cytosolic Nudix hydrolases in Arabidopsis thaliana. J Biol Chem. 2005 Jul 1;280(26):25277-83. Epub 2005 May 5. PMID:15878881 doi:http://dx.doi.org/M503536200
↑ Yoshimura K, Ogawa T, Ueda Y, Shigeoka S. AtNUDX1, an 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate pyrophosphohydrolase, is responsible for eliminating oxidized nucleotides in Arabidopsis. Plant Cell Physiol. 2007 Oct;48(10):1438-49. Epub 2007 Sep 5. PMID:17804481 doi:http://dx.doi.org/10.1093/pcp/pcm112
↑ Henry LK, Thomas ST, Widhalm JR, Lynch JH, Davis TC, Kessler SA, Bohlmann J, Noel JP, Dudareva N. Contribution of isopentenyl phosphate to plant terpenoid metabolism. Nat Plants. 2018 Sep;4(9):721-729. doi: 10.1038/s41477-018-0220-z. Epub 2018 Aug , 20. PMID:30127411 doi:http://dx.doi.org/10.1038/s41477-018-0220-z

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/6dbz"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Nudix 1 from Arabidopsis thaliana complexed with isopentenyl diphosphate==
-<StructureSection load='6dbz' size='340' side='right' caption='[[6dbz]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='6dbz' size='340' side='right'caption='[[6dbz]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6dbz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6dbz]] is a 2 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=6DBZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DBZ FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IPR:ISOPENTYL+PYROPHOSPHATE'>IPR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[pdb|pdb]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6dby|6dby]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NUDT1, NUDX1, At1g68760, F14K14.13 ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dbz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dbz OCA], [http://pdbe.org/6dbz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dbz RCSB], [http://www.ebi.ac.uk/pdbsum/6dbz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dbz ProSAT]</span></td></tr>
 </table>
@@ Line 19: / Line 20: @@
 </div>
 <div class="pdbe-citations 6dbz" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Nudix hydrolase 3D structures|Nudix hydrolase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Arath]]
+[[Category: Large Structures]]
 [[Category: Dudareva, N]]
 [[Category: Henry, L K]]

6dbz

From Proteopedia

Revision as of 17:18, 20 November 2019

Crystal structure of Nudix 1 from Arabidopsis thaliana complexed with isopentenyl diphosphate

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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