5NHG | pdb_00005nhg

Crystal structure of the human dihydrolipoamide dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb5NHG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-21 Released: 2018-05-16
Deposition Author(s): Szabo, E., Mizsei, R., Wilk, P., Zambo, Z., Torocsik, B., Weiss, M.S., Adam-Vizi, V., Ambrus, A.
Funding Organization(s): Hungarian Academy of Sciences, Hungarian Scientific Research Fund, Hungarian Brain Research Program, European Molecular Biology Organization, Helmholtz-Zentrum Berlin

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.180 (Depositor), 0.182 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 427.4 kDa
Atom Count: 28,780
Modeled Residue Count: 3,771
Deposited Residue Count: 3,960
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase, mitochondrial	A, B, C, D, E A, B, C, D, E, F, G, H	495	Homo sapiens	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09622
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain X [auth H] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G] mmCIF format, chain X [auth H]	I [auth A] L [auth B] M [auth C] P [auth D] Q [auth E] I [auth A], L [auth B], M [auth C], P [auth D], Q [auth E], T [auth F], V [auth G], X [auth H]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain O [auth C] MOL2 format, chain O [auth C] mmCIF format, chain O [auth C]	O [auth C]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Interactions & Density Focus chain O [auth C]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth C] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain W [auth G] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth C] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain W [auth G] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth C] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain W [auth G]	J [auth A] K [auth A] N [auth C] R [auth E] S [auth E] J [auth A], K [auth A], N [auth C], R [auth E], S [auth E], U [auth F], W [auth G]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.210 (Depositor), 0.210 (DCC)
R-Value Work: 0.180 (Depositor), 0.182 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.06	α = 83.18
b = 113.54	β = 84.75
c = 136.88	γ = 81.09

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Hungarian Academy of Sciences	Hungary	02001
Hungarian Scientific Research Fund	Hungary	112230
Hungarian Brain Research Program	Hungary	KTIA_13_NAP-A-III/6
Hungarian Academy of Sciences	Hungary	Bolyai Fellowship [to A.A.]
European Molecular Biology Organization	Hungary	Short-term Fellowship [to A.A.]
Helmholtz-Zentrum Berlin	Germany	16204087-ST, BESSY: 362 [to E.Sz., A.A.]

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2018-07-04
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary