3NPE | pdb_00003npe

Structure of VP14 in complex with oxygen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.272 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3NPE

This is version 1.4 of the entry. See complete history

Literature

Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid.

Messing, S.A.Gabelli, S.B.Echeverria, I.Vogel, J.T.Guan, J.C.Tan, B.C.Klee, H.J.McCarty, D.R.Amzel, L.M.

(2010) Plant Cell 22: 2970-2980

  • DOI: https://doi.org/10.1105/tpc.110.074815
  • Primary Citation Related Structures: 
    3NPE

  • PubMed Abstract: 

    The key regulatory step in the biosynthesis of abscisic acid (ABA), a hormone central to the regulation of several important processes in plants, is the oxidative cleavage of the 11,12 double bond of a 9-cis-epoxycarotenoid. The enzyme viviparous14 (VP14) performs this cleavage in maize (Zea mays), making it a target for the rational design of novel chemical agents and genetic modifications that improve plant behavior through the modulation of ABA levels. The structure of VP14, determined to 3.2-Å resolution, provides both insight into the determinants of regio- and stereospecificity of this enzyme and suggests a possible mechanism for oxidative cleavage. Furthermore, mutagenesis of the distantly related CCD1 of maize shows how the VP14 structure represents a template for all plant carotenoid cleavage dioxygenases (CCDs). In addition, the structure suggests how VP14 associates with the membrane as a way of gaining access to its membrane soluble substrate.


  • Organizational Affiliation
    • Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA.

Macromolecule Content 

  • Total Structure Weight: 58.02 kDa 
  • Atom Count: 4,042 
  • Modeled Residue Count: 522 
  • Deposited Residue Count: 529 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
9-cis-epoxycarotenoid dioxygenase 1, chloroplastic529Zea maysMutation(s): 0 
Gene Names: VP14
EC: 1.13.11.51
Membrane Entity: Yes 
UniProt
Find proteins for O24592 (Zea mays)
Explore O24592 
Go to UniProtKB:  O24592
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO24592
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DIO

Query on DIO



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
OXY

Query on OXY



Download:Ideal Coordinates CCD File
C [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
OH

Query on OH



Download:Ideal Coordinates CCD File
D [auth A]HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.272 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.521α = 90
b = 161.521β = 90
c = 150.816γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-11-20
    Changes: Structure summary