5JCI

Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica

Park, A.K.Kim, I.S.Do, H.Jeon, B.W.Lee, C.W.Roh, S.J.Shin, S.C.Park, H.Kim, Y.S.Kim, Y.H.Yoon, H.S.Lee, J.H.Kim, H.W.

(2016) Sci Rep 6: 33903-33903

  • DOI: 10.1038/srep33903
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ascorbic acid (AsA) maintains redox homeostasis by scavenging reactive oxygen species from prokaryotes to eukaryotes, especially plants. The enzyme monodehydroascorbate reductase (MDHAR) regenerates AsA by catalysing the reduction of monodehydroascor ...

    Ascorbic acid (AsA) maintains redox homeostasis by scavenging reactive oxygen species from prokaryotes to eukaryotes, especially plants. The enzyme monodehydroascorbate reductase (MDHAR) regenerates AsA by catalysing the reduction of monodehydroascorbate, using NADH or NADPH as an electron donor. The detailed recycling mechanism of MDHAR remains unclear due to lack of structural information. Here, we present the crystal structures of MDHAR in the presence of cofactors, nicotinamide adenine dinucleotide (NAD + ) and nicotinamide adenine dinucleotide phosphate (NADP + ), and complexed with AsA as well as its analogue, isoascorbic acid (ISD). The overall structure of MDHAR is similar to other iron-sulphur protein reductases, except for a unique long loop of 63-80 residues, which seems to be essential in forming the active site pocket. From the structural analysis and structure-guided point mutations, we found that the Arg320 residue plays a major substrate binding role, and the Tyr349 residue mediates electron transfer from NAD(P)H to bound substrate via FAD. The enzymatic activity of MDHAR favours NADH as an electron donor over NADPH. Our results show, for the first time, structural insights into this preference. The MDHAR-ISD complex structure revealed an alternative binding conformation of ISD, compared with the MDHAR-AsA complex. This implies a broad substrate (antioxidant) specificity and resulting greater protective ability of MDHAR.


    Organizational Affiliation

    Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea.,Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea.,Research Institute for Ulleung-do &Dok-do, Kyungpook National University, Daegu 41566, Republic of Korea.,Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang 25342, Republic of Korea.,School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Os09g0567300 protein
A
453Oryza sativa subsp. japonicaMutation(s): 0 
Gene Names: MDAR3 (MDHAR3)
EC: 1.6.5.4
Find proteins for Q652L6 (Oryza sativa subsp. japonica)
Go to UniProtKB:  Q652L6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.143 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.270α = 90.00
b = 81.270β = 90.00
c = 120.665γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-04-15 
  • Released Date: 2016-10-12 
  • Deposition Author(s): Park, A.K., Kim, H.W.

Funding OrganizationLocationGrant Number
Korea Polar Research InstituteKorea, Republic OfPE16070

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release