7MDH | pdb_00007mdh

STRUCTURAL BASIS FOR LIGHT ACITVATION OF A CHLOROPLAST ENZYME. THE STRUCTURE OF SORGHUM NADP-MALATE DEHYDROGENASE IN ITS OXIDIZED FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.221 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7MDH

This is version 1.5 of the entry. See complete history

Literature

Structural basis for light activation of a chloroplast enzyme: the structure of sorghum NADP-malate dehydrogenase in its oxidized form.

Johansson, K.Ramaswamy, S.Saarinen, M.Lemaire-Chamley, M.Issakidis-Bourguet, E.Miginiac-Maslow, M.Eklund, H.

(1999) Biochemistry 38: 4319-4326

  • DOI: https://doi.org/10.1021/bi982876c
  • Primary Citation Related Structures: 
    7MDH

  • PubMed Abstract: 

    Some key chloroplast enzymes are activated by light via a ferredoxin-thioredoxin reduction system which reduces disulfide bridges in the enzymes. We describe for the first time the structural basis for the redox activation of a chloroplast enzyme, the NADP-dependent malate dehydrogenase (MDH) from Sorghum vulgare whose structure has been determined and refined at 2.4 A resolution. In addition to the normal structural components of MDHs, the enzyme exhibits extensions at both the N- and C-termini, each of which contains a regulatory disulfide bridge which must be reduced for activation. The N-terminal disulfide motif is inserted in a cleft between the two subunits of the dimer, thereby locking the domains in each subunit. The C-terminal disulfide keeps the C-terminal residues tight to the enzyme surface and blocks access to the active site. Reduction of the N-terminal disulfide would release the stopper between the domains and give the enzyme the necessary flexibility. Simultaneous reduction of the C-terminal disulfide would free the C-terminal residues from binding to the enzyme and make the active site accessible.


  • Organizational Affiliation
    • Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala.

Macromolecule Content 

  • Total Structure Weight: 164.58 kDa 
  • Atom Count: 11,132 
  • Modeled Residue Count: 1,415 
  • Deposited Residue Count: 1,500 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (MALATE DEHYDROGENASE)
A, B, C, D
375Sorghum bicolorMutation(s): 0 
EC: 1.1.1.82
UniProt
Find proteins for P17606 (Sorghum bicolor)
Explore P17606 
Go to UniProtKB:  P17606
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17606
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
U [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.424α = 90
b = 153.944β = 90
c = 160.042γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-04
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-30
    Changes: Structure summary