6DBY

Crystal structure of Nudix 1 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Contribution of isopentenyl phosphate to plant terpenoid metabolism.

Henry, L.K.Thomas, S.T.Widhalm, J.R.Lynch, J.H.Davis, T.C.Kessler, S.A.Bohlmann, J.Noel, J.P.Dudareva, N.

(2018) Nat Plants 4: 721-729

  • DOI: 10.1038/s41477-018-0220-z
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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. ...

    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.


    Organizational Affiliation

    Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA. dudareva@purdue.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nudix hydrolase 1
A, B
150Arabidopsis thalianaMutation(s): 0 
Gene Names: NUDT1NUDX1At1g68760F14K14.13
EC: 3.6.1.55 (PDB Primary Data), 3.6.1.67 (PDB Primary Data), 3.6.1.22 (PDB Primary Data)
Find proteins for Q9CA40 (Arabidopsis thaliana)
Go to UniProtKB:  Q9CA40
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.19α = 90
b = 73.07β = 90
c = 116.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
BOSdata collection

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesEEC-0813570

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence