PDB-6i4u: Crystal structure of the disease-causing G426E mutant of the huma...

ID or keywords:

Entry

Database: PDB / ID: 6i4u

Title

Crystal structure of the disease-causing G426E mutant of the human dihydrolipoamide dehydrogenase

Components

Dihydrolipoyl dehydrogenase, mitochondrial

Dihydrolipoamide dehydrogenase

Keywords

OXIDOREDUCTASE /

Lipoamide dehydrogenase / Pathogenic mutation / E3 deficiency /

Alpha-ketoglutarate dehydrogenase complex /

2-oxoglutarate dehydrogenase complex /

Pyruvate dehydrogenase complex

Function / homology

Function and homology information

acetyltransferase complex / acrosomal matrix / Glycine degradation / : /

dihydrolipoyl dehydrogenase /

dihydrolipoyl dehydrogenase activity /

oxoglutarate dehydrogenase complex / acetyl-CoA biosynthetic process from pyruvate /

pyruvate dehydrogenase complex /

: ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.84 Å

Authors

Szabo, E. / Wilk, P. / Hubert, A. / Torocsik, B. / Weiss, M.S. / Adam-Vizi, V. / Ambrus, A.

Funding support

Hungary,

United States,

Germany, 10items

Organization	Grant number	Country
Hungarian Academy of Sciences	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.]	Hungary
Hungarian Academy of Sciences	Bolyai Fellowship [to A.A.]	Hungary
European Molecular Biology Organization	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.]	Hungary
	Fulbright Commission, Fulbright Fellowship [to A.A.]	United States
	European Union and Government of Hungary, grant#EFOP-3.6.3-VEKOP-16-2017-00009 [to S.E.]	Hungary
	European Union CALIPSOplus, grant#16204087-ST [to S.E. and A.A.]	Germany

Citation

Journal: Hum.Mol.Genet. / Year: 2019
Title: Underlying molecular alterations in human dihydrolipoamide dehydrogenase deficiency revealed by structural analyses of disease-causing enzyme variants.
Authors: 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.

History

Deposition	Nov 10, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2019	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6i4u.cif.gz	542.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6i4u.ent.gz	453.7 KB	Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i4/6i4u ftp://data.pdbj.org/pub/pdb/validation_reports/i4/6i4u	HTTPS FTP

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Related structure data

Related structure data	6i4pC 6i4qC 6i4rC 6i4sC 6i4tC 6i4zC 1zmdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5j5z-d 5nhg-2 6i4z-2 1zmc-2 5u8u-1 2a8x-d 7kmy-2 4jq9-2 3l8k-d 5nhg-4 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (11) #154 - Oct 2012 Citric Acid Cycle similarity (10) #155 - Nov 2012 Vitamin D Receptor similarity (2) #82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: Dihydrolipoyl dehydrogenase, mitochondrial

B: Dihydrolipoyl dehydrogenase, mitochondrial

hetero molecules

108 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	118.737, 168.663, 61.041
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Dihydrolipoyl dehydrogenase, mitochondrial / Dihydrolipoamide dehydrogenase / Dihydrolipoamide dehydrogenase / Glycine cleavage system L protein Mass: 52709.234 Da / Num. of mol.: 2 / Mutation: G426E Source method: isolated from a genetically manipulated source Details: Sequence of the Strep-tag with linker amino acids: MASWSHPQFEKGALEVLFQGPG Source: (gene. exp.) Homo sapiens (human) / Gene: DLD, GCSL, LAD, PHE3 / Plasmid: pET52b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09622, dihydrolipoyl dehydrogenase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3 Å³/Da / Density % sol: 58.99 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2 M ammonium sulfate, 2(v/v)% PEG 400, 0.1 M Hepes (pH 7.5)

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.9184 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9184 Å / Relative weight: 1

Reflection

Resolution: 1.84→42.559 Å / Num. obs: 106853 / % possible obs: 99.2 % / Redundancy: 6.658 % / B_iso Wilson estimate: 28.8 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.098 / R_rim(I) all: 0.106 / Χ²: 1.13 / Net I/σ(I): 13.27

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.84-1.95	6.811	1.307	1.24	16793	0.807	1.414	97.5
1.95-2.08	6.715	0.797	2.08	16102	0.917	0.864	99.5
2.08-2.25	6.48	0.43	3.83	14998	0.968	0.467	99.4
2.25-2.46	6.923	0.27	6.32	13884	0.986	0.291	99.7
2.46-2.75	6.654	0.162	10.28	12632	0.993	0.176	99.7
2.75-3.18	6.76	0.092	18.32	11164	0.997	0.1	99.7
3.18-3.89	6.583	0.052	33.71	9525	0.999	0.057	99.8
3.89-5.48	6.306	0.035	46.63	7434	0.999	0.039	99.2
5.48-42.559	6.138	0.027	50.11	4320	1	0.029	98.7

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R rigid body: 0.604

	Highest resolution	Lowest resolution
Rotation	48.63 Å	2.26 Å

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX		refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ZMD

1zmd

Resolution: 1.84→42.559 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.97
Details: TLS groups, NCS torsion-angle restraints, automatic occupancy refinement and real-space refinement were involved, hydrogen atoms were added to the final model during refinement

	R_factor	Num. reflection	% reflection
R_free	0.2006	2094	1.96 %
R_work	0.1838	-	-
obs	0.1841	106633	99.02 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.84→42.559 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7096	0	167	347	7610

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7508
X-RAY DIFFRACTION	f_angle_d	0.807	10195
X-RAY DIFFRACTION	f_dihedral_angle_d	14.563	4489
X-RAY DIFFRACTION	f_chiral_restr	0.052	1163
X-RAY DIFFRACTION	f_plane_restr	0.005	1301

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.84-1.8792	0.3807	130	0.3712	6510	X-RAY DIFFRACTION	94
1.8792-1.9262	0.3915	137	0.341	6903	X-RAY DIFFRACTION	100
1.9262-1.9782	0.3299	140	0.2982	6947	X-RAY DIFFRACTION	99
1.9782-2.0365	0.3036	137	0.2642	6888	X-RAY DIFFRACTION	99
2.0365-2.1022	0.2624	137	0.2432	6917	X-RAY DIFFRACTION	99
2.1022-2.1773	0.2685	139	0.2151	6883	X-RAY DIFFRACTION	99
2.1773-2.2645	0.2054	140	0.1927	6977	X-RAY DIFFRACTION	99
2.2645-2.3675	0.2234	139	0.1807	6915	X-RAY DIFFRACTION	100
2.3675-2.4923	0.1911	140	0.1795	6968	X-RAY DIFFRACTION	100
2.4923-2.6485	0.1978	140	0.1758	7003	X-RAY DIFFRACTION	99
2.6485-2.8529	0.2161	141	0.1826	7004	X-RAY DIFFRACTION	100
2.8529-3.1399	0.1741	141	0.1871	7031	X-RAY DIFFRACTION	100
3.1399-3.5941	0.2049	142	0.177	7124	X-RAY DIFFRACTION	100
3.5941-4.5274	0.1443	142	0.1386	7075	X-RAY DIFFRACTION	99
4.5274-42.559	0.1733	149	0.1584	7394	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.2288	0.6679	1.1704	1.9264	0.1556	1.8299	0.1266	-0.1776	0.2066	0.3177	-0.0533	0.2921	-0.0587	-0.1701	0.0053	0.3077	0.0106	0.1413	0.1982	-0.0027	0.308	34.8064	9.2029	23.9249
2	1.7244	0.5659	0.1009	2.8711	-0.4851	0.22	0.0616	-0.0852	0.3378	-0.0227	0.0029	0.8461	0.0448	-0.2973	-0.0219	0.3218	-0.0196	0.1584	0.2814	0.0577	0.4324	19.9411	-1.0417	21.135
3	1.2243	0.4207	0.5022	2.0542	-0.2034	0.6863	-0.1141	-0.077	0.4828	-0.0318	0.063	0.3297	-0.1847	-0.1427	0.0683	0.3236	0.0338	0.0941	0.2201	0.0254	0.4211	33.8498	19.2701	16.6037
4	1.7333	-0.7751	0.7862	2.4226	-0.7452	1.0185	0.0116	0.3329	0.1694	-0.8751	0.0751	0.3687	0.216	0.0003	-0.0721	0.6061	-0.0721	-0.046	0.2952	0.0856	0.3379	27.8433	2.949	-2.4362
5	1.6268	0.6495	0.5229	2.3994	0.0674	0.8697	-0.0458	0.1525	0.1946	-0.1561	0.0569	-0.1331	-0.0482	0.0416	-0.0122	0.3214	0.0059	0.1228	0.2085	0.0273	0.3264	45.2664	12.5347	12.7492
6	1.0232	0.3415	0.794	1.9645	-0.1016	1.0603	-0.0315	0.209	-0.3067	-0.4629	0.1403	-0.3855	0.073	0.0634	-0.0375	0.3918	-0.0216	0.1169	0.2273	-0.0491	0.3492	43.8623	-15.8498	8.7632
7	1.1374	-0.551	-0.0226	2.7146	0.0658	0.591	0.0807	0.1124	-0.1741	-0.3024	0.0996	0.32	0.0889	-0.0598	-0.1772	0.4328	-0.0658	-0.0513	0.2885	0.0107	0.4245	28.7523	-32.1081	12.0012
8	1.2178	0.0853	-0.4046	1.8584	0.259	1.1381	0.1243	-0.1511	-0.27	0.3379	0.0602	0.0649	0.1905	0.0281	-0.1754	0.4555	-0.0484	-0.0314	0.2279	0.0618	0.3897	31.8221	-37.7759	27.9087
9	1.7162	0.3147	-0.4694	3.7033	-0.3617	1.0237	0.1113	-0.2015	0.0131	0.4749	-0.0746	-0.2065	-0.0021	-0.0154	-0.0583	0.3987	-0.0215	0.0155	0.2153	-0.0056	0.2525	41.7027	-11.4386	30.2873

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 67 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 68 through 110 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 111 through 187 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 188 through 260 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 261 through 358 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 359 through 474 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -7 through 110 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 111 through 358 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 359 through 474 )

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