5J5Z | pdb_00005j5z

Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb5J5Z/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-04-04 Released: 2017-11-15 
• Deposition Author(s): Szabo, E., Mizsei, R., Zambo, Z., Torocsik, B., Weiss, M.S., Adam-Vizi, V., Ambrus, A.
• Funding Organization(s): Hungarian Academy of Sciences (MTA), Hungarian Scientific Research Fund (OTKA), Hungarian Brain Research Program (NAP), European Molecular Biology Organization, Hungarian Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of the disease-causing D444V mutant and the relevant wild type human dihydrolipoamide dehydrogenase.

Szabo, E., Mizsei, R., Wilk, P., Zambo, Z., Torocsik, B., Weiss, M.S., Adam-Vizi, V., Ambrus, A.

(2018) Free Radic Biol Med 124: 214-220

• PubMed: 29908278 
• DOI: https://doi.org/10.1016/j.freeradbiomed.2018.06.008
• Primary Citation Related Structures: 
  5J5Z, 5NHG


• PubMed Abstract: 
  

  We report the crystal structures of the human (dihydro)lipoamide dehydrogenase (hLADH, hE3) and its disease-causing homodimer interface mutant D444V-hE3 at 2.27 and 1.84 Å resolution, respectively. The wild type structure is a unique uncomplexed, unliganded hE3 structure with the true canonical sequence. Based on the structural information a novel molecular pathomechanism is proposed for the impaired catalytic activity and enhanced capacity for reactive oxygen species generation of the pathogenic mutant. The mechanistic model involves a previously much ignored solvent accessible channel leading to the active site that might be perturbed also by other disease-causing homodimer interface substitutions of this enzyme.

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Organizational Affiliation: 
• Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, H-1094 Budapest, Hungary.
Macromolecular Crystallography, Helmholtz-Zentrum Berlin für Materialien und Energie, D-12489 Berlin, Germany.
Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, H-1094 Budapest, Hungary. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 107.28 kDa 
• Atom Count: 7,848 
• Modeled Residue Count: 959 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase, mitochondrial	A, B	496	Homo sapiens	Mutation(s): 1  Gene Names: DLD, GCSL, LAD, PHE3 EC: 1.8.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for P09622 (Homo sapiens) Explore P09622  Go to UniProtKB:  P09622
PHAROS:  P09622 GTEx:  ENSG00000091140

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PO4	D [auth A], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.035	α = 90
b = 168.939	β = 90
c = 61.279	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Szabo, E., Mizsei, R., Zambo, Z., Torocsik, B., Weiss, M.S., Adam-Vizi, V., Ambrus, A.

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Funding Organization	Location	Grant Number
Hungarian Academy of Sciences (MTA)	Hungary	02001
Hungarian Scientific Research Fund (OTKA)	Hungary	112230
Hungarian Brain Research Program (NAP)	Hungary	KTIA_13_NAP_A_III/6
European Molecular Biology Organization	Hungary	Short-term Fellowship [to A.A.]
Hungarian Academy of Sciences	Hungary	Bolyai Fellowship [to A.A]

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2018-03-28
  Changes: Source and taxonomy
• Version 1.2: 2018-07-04
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2018-07-11
  Changes: Data collection, Database references
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary