6I4T

Crystal structure of the disease-causing I445M mutant of the human dihydrolipoamide dehydrogenase

• PDB DOI:  https://doi.org/10.2210/pdb6I4T/pdb

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


• Deposited: 2018-11-10 Released: 2019-11-20 
• Deposition Author(s): Szabo, E., Wilk, P., Zambo, Z., Torocsik, B., Weiss, M.S., Adam-Vizi, V., Ambrus, A.
• Funding Organization(s): Hungarian Academy of Sciences, European Molecular Biology Organization

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.210 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 

Literature

Underlying molecular alterations in human dihydrolipoamide dehydrogenase deficiency revealed by structural analyses of disease-causing enzyme variants.

Szabo, E., Wilk, P., Nagy, B., Zambo, Z., Bui, D., Weichsel, A., Arjunan, P., Torocsik, B., Hubert, A., Furey, W., Montfort, W.R., Jordan, F., Weiss, M.S., Adam-Vizi, V., Ambrus, A.

(2019) Hum Mol Genet 28: 3339-3354

• PubMed: 31334547 
• DOI: https://doi.org/10.1093/hmg/ddz177
• Primary Citation of Related Structures:  
  6I4P, 6I4Q, 6I4R, 6I4S, 6I4T, 6I4U, 6I4Z


• PubMed Abstract: 
  

Human dihydrolipoamide dehydrogenase (hLADH, hE3) deficiency (OMIM# 246900) is an often prematurely lethal genetic disease usually caused by inactive or partially inactive hE3 variants. Here we report the crystal structure of wild-type hE3 at an unprecedented high resolution of 1.75 Å and the structures of six disease-causing hE3 variants at resolutions ranging from 1.44 to 2.34 Å. P453L proved to be the most deleterious substitution in structure as aberrations extensively compromised the active site. The most prevalent G194C-hE3 variant primarily exhibited structural alterations close to the substitution site, whereas the nearby cofactor-binding residues were left unperturbed. The G426E substitution mainly interfered with the local charge distribution introducing dynamics to the substitution site in the dimer interface; G194C and G426E both led to minor structural changes. The R460G, R447G and I445M substitutions all perturbed a solvent accessible channel, the so-called H+/H2O channel, leading to the active site. Molecular pathomechanisms of enhanced reactive oxygen species (ROS) generation and impaired binding to multienzyme complexes were also addressed according to the structural data for the relevant mutations. In summary, we present here for the first time a comprehensive study that links three-dimensional structures of disease-causing hE3 variants to residual hLADH activities, altered capacities for ROS generation, compromised affinities for multienzyme complexes and eventually clinical symptoms. Our results may serve as useful starting points for future therapeutic intervention approaches.

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Organizational Affiliation: 

Department of Medical Biochemistry, MTA-SE Laboratory for Neurobiochemistry, Semmelweis University, Budapest, 1094, Hungary.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 107.89 kDa 
• Atom Count: 7,732 
• Modelled Residue Count: 953 
• 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], I [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
1PE	H [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.210 
• R-Value Work: 0.191 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.915	α = 90
b = 169.004	β = 90
c = 60.831	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Szabo, E., Wilk, P., 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	Hungary	02001 [to A.-V.V.]
	Hungary	Hungarian Scientific Research Fund, grant#112230 [to A.-V.V.]
	Hungary	Hungarian Brain Research Program, grant#KTIA_13_NAP_III/6 and 2017-1.2.1-NKP-2017-00002 [to A.-V.V.]
Hungarian Academy of Sciences	Hungary	Bolyai Fellowship [to A.A.]
European Molecular Biology Organization	Hungary	Short-term Fellowship [to A.A.]
	Hungary	Semmelweis University, Young Investigator Research Grant [to A.A.]
	Hungary	Gedeon Richter PIc., Young Investigator Research Grant [to A.A.]
	United States	Fulbright Commission, Fulbright Fellowship [to A.A.]
	Hungary	European Union and Government of Hungary, grant#EFOP-3.6.3-VEKOP-16-2017-00009 [to S.E.]
	Germany	European Union CALIPSOplus, grant#16204087-ST [to S.E. and A.A.]

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Database references