8FF7

Cytosolic ascorbate peroxidase mutant from Panicum virgatum- ascorbate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Activity of Cytosolic Ascorbate Peroxidase (APX) from Panicum virgatum against Ascorbate and Phenylpropanoids.

Zhang, B.Lewis, J.A.Kovacs, F.Sattler, S.E.Sarath, G.Kang, C.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24021778
  • Primary Citation of Related Structures:  
    8FF6, 8FF7

  • PubMed Abstract: 

    APX is a key antioxidant enzyme in higher plants, scavenging H 2 O 2 with ascorbate in several cellular compartments. Here, we report the crystal structures of cytosolic ascorbate peroxidase from switchgrass ( Panicum virgatum L., Pvi ), a strategic feedstock plant with several end uses. The overall structure of PviAPX was similar to the structures of other APX family members, with a bound ascorbate molecule at the ɣ-heme edge pocket as in other APXs. Our results indicated that the H 2 O 2 -dependent oxidation of ascorbate displayed positive cooperativity. Significantly, our study suggested that PviAPX can oxidize a broad range of phenylpropanoids with δ-meso site in a rather similar efficiency, which reflects its role in the fortification of cell walls in response to insect feeding. Based on detailed structural and kinetic analyses and molecular docking, as well as that of closely related APX enzymes, the critical residues in each substrate-binding site of PviAPX are proposed. Taken together, these observations shed new light on the function and catalysis of PviAPX, and potentially benefit efforts improve plant health and biomass quality in bioenergy and forage crops.


  • Organizational Affiliation

    Department of Chemistry, Washington State University, Pullman, WA 99164, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosolic ascorbate peroxidase
A, B, C, D, E
A, B, C, D, E, F
250Panicum virgatumMutation(s): 5 
Gene Names: PVAP13_9KG480900
UniProt
Find proteins for A0A8T0NWI5 (Panicum virgatum)
Explore A0A8T0NWI5 
Go to UniProtKB:  A0A8T0NWI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8T0NWI5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
N [auth C]
Q [auth D]
T [auth E]
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
T [auth E],
W [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ASC
Query on ASC

Download Ideal Coordinates CCD File 
G [auth A]
J [auth B]
M [auth C]
P [auth D]
S [auth E]
G [auth A],
J [auth B],
M [auth C],
P [auth D],
S [auth E],
V [auth F]
ASCORBIC ACID
C6 H8 O6
CIWBSHSKHKDKBQ-JLAZNSOCSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
O [auth C]
R [auth D]
U [auth E]
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.267α = 104.55
b = 80.176β = 101.97
c = 80.166γ = 110.73
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-1804699
National Science Foundation (NSF, United States)United StatesMCB-2043248

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description