Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.02 kDa 
• Atom Count: 4042 
• Modelled Residue Count: 522 
• Deposited Residue Count: 529 
• Unique protein chains: 1

3NPE

Structure of VP14 in complex with oxygen

• DOI: 10.2210/pdb3NPE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-28 Released: 2010-11-10 
• Deposition Author(s): Messing, S.A., Gabelli, S.B., Amzel, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.272 
• R-Value Work: 0.241 
• R-Value Observed: 0.242 

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

• PubMed: 20884803 
• DOI: 10.1105/tpc.110.074815
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
9-cis-epoxycarotenoid dioxygenase 1, chloroplastic	A	529	Zea mays	Mutation(s): 0  Gene Names: VP14 EC: 1.13.11.51
Find proteins for O24592 (Zea mays) Explore O24592  Go to UniProtKB:  O24592

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIO	A	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N
FE2	A	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
OXY	A	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N
OH	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 
• R-Value Work: 0.241 
• R-Value Observed: 0.242 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.521	α = 90
b = 161.521	β = 90
c = 150.816	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-28 
• Released Date: 2010-11-10 
Deposition Author(s): Messing, S.A., Gabelli, S.B., Amzel, L.M.

Revision History  

• 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