PDB-3crk: Crystal structure of the PDHK2-L2 complex.

ID or keywords:

Entry

Database: PDB / ID: 3crk

Title

Crystal structure of the PDHK2-L2 complex.

Components

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrialDihydrolipoyl transacetylase
Pyruvate dehydrogenase [lipoamide] kinase isozyme 2, mitochondrial

Keywords

TRANSFERASE / pyruvate dehydrogenase kinase isozyme 2 /

glucose metabolism /

kinase /

mitochondrion /

Carbohydrate metabolism / Transit peptide /

Acyltransferase /

Glycolysis / Lipoyl

Function / homology

Function and homology information

Signaling by Retinoic Acid / Regulation of pyruvate dehydrogenase (PDH) complex / [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate /

dihydrolipoyllysine-residue acetyltransferase /

dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase (acetyl-transferring) kinase activity / acetyl-CoA biosynthetic process from pyruvate /

pyruvate dehydrogenase complex /

: ...
Similarity search - Function

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain / Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal / Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily / PDK/BCKDK protein kinase / Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase /

Peripheral subunit-binding domain / e3 binding domain /

Peripheral subunit-binding (PSBD) domain profile. ...
Similarity search - Domain/homology

Biological species

Rattus norvegicus (Norway rat)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

Green, T.J. / Popov, K.M. / Luo, M. / Grigorian, A. / Klyuyeva, A. / Tuganova, A.

Citation

Journal: J.Biol.Chem. / Year: 2008
Title: Structural and functional insights into the molecular mechanisms responsible for the regulation of pyruvate dehydrogenase kinase 2.
Authors: Green, T. / Grigorian, A. / Klyuyeva, A. / Tuganova, A. / Luo, M. / Popov, K.M.

History

Deposition	Apr 7, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3crk.cif.gz	191 KB	Display	PDBx/mmCIF format
PDB format	pdb3crk.ent.gz	160.3 KB	Display	PDB format
PDBx/mmJSON format	3crk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cr/3crk ftp://data.pdbj.org/pub/pdb/validation_reports/cr/3crk	HTTPS FTP

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Related structure data

Related structure data	3crlC C: citing same article (ref.)
Similar structure data	1y8p-1 3crl-d 1y8n-1 2q8i-1 1y8o-1 4fxd-1 3e2e-d 3ctm-1 1h4t-2 1ewk-d 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 (14) #154 - Oct 2012 Citric Acid Cycle similarity (13) #190 - Oct 2015 Two-component Systems similarity (2) #155 - Nov 2012 Vitamin D Receptor similarity (2) #183 - Mar 2015 Phototropin similarity (2)

Deposited unit

A: Pyruvate dehydrogenase [lipoamide] kinase isozyme 2, mitochondrial

B: Pyruvate dehydrogenase [lipoamide] kinase isozyme 2, mitochondrial

C: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial

D: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial

hetero molecules

112 kDa, 4 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)	71.380, 120.679, 71.466
Angle α, β, γ (deg.)	90.000, 96.030, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pyruvate dehydrogenase [lipoamide] kinase isozyme 2, mitochondrial / Pyruvate dehydrogenase kinase isoform 2 / PDK P45 Mass: 46155.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pdk2 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q64536, [pyruvate dehydrogenase (acetyl-transferring)] kinase
#2: Protein	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial / Dihydrolipoyl transacetylase / Pyruvate dehydrogenase complex E2 subunit / PDCE2 / E2 / Dihydrolipoamide S- acetyltransferase ...Pyruvate dehydrogenase complex E2 subunit / PDCE2 / E2 / Dihydrolipoamide S- acetyltransferase component of pyruvate dehydrogenase complex / PDC- E2 / 70 kDa mitochondrial autoantigen of primary biliary cirrhosis / PBC / M2 antigen complex 70 kDa subunit Mass: 9764.351 Da / Num. of mol.: 2 / Fragment: UNP residues 181-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLAT, DLTA / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P10515, dihydrolipoyllysine-residue acetyltransferase
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.81 Å³/Da / Density % sol: 56.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3 Details: 0.1 M sodium acetate (pH 5.3) and 0.5 M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97625 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.3→71.07 Å / Num. obs: 50377 / % possible obs: 94.9 % / R_merge(I) obs: 0.055 / Net I/σ(I): 18.8
Reflection shell	Resolution: 2.3→2.3 Å / R_merge(I) obs: 0.269 / Mean I/σ(I) obs: 3.2 / % possible all: 73.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
COMO		phasing
REFMAC	5.2.0005	refinement
PDB_EXTRACT	3.005	data extraction
MAR345		data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.906 / SU B: 12.907 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2506	2551	5.1 %	RANDOM
R_work	0.2078	-	-	-
obs	0.21	50377	94.94 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 53.273 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.12 Å²	0 Å²	0.11 Å²
2-	-	0.72 Å²	0 Å²
3-	-	-	-0.58 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7221	0	2	267	7490

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	7385
X-RAY DIFFRACTION	r_angle_refined_deg	1.009	1.979	10012
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.081	5	897
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.318	24.479	326
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.46	15	1280
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.244	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1126
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	5526
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	3447
X-RAY DIFFRACTION	r_nbtor_refined	0.301	0.2	5007
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	409
X-RAY DIFFRACTION	r_metal_ion_refined	0.232	0.2	5
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.108	0.2	60
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.139	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	0.285	1.5	4528
X-RAY DIFFRACTION	r_mcangle_it	0.554	2	7365
X-RAY DIFFRACTION	r_scbond_it	0.933	3	2899
X-RAY DIFFRACTION	r_scangle_it	1.522	4.5	2647

LS refinement shell

Resolution: 2.3→2.365 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	140	-
R_work	0.233	2621	-
all	-	2761	-
obs	-	-	71.44 %

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	2.0731	-0.9397	-0.6856	2.425	0.5956	4.076	-0.0964	-0.2813	-0.12	0.3376	-0.0126	-0.1908	0.3468	-0.0016	0.109	0.2483	-0.0255	0.0283	-0.0678	0.0348	-0.2221	68.2863	94.8243	70.4345
2	2.7407	0.7129	0.1997	5.7127	-0.5329	3.2633	-0.1031	-0.2452	0.1613	0.7638	-0.0107	0.0212	-0.0776	-0.4415	0.1139	0.3058	-0.0203	0.038	0.1141	-0.0354	-0.2576	62.2031	99.8754	71.6243
3	3.0046	2.385	1.1393	8.2455	-0.0385	1.7007	-0.0202	-0.1997	0.0202	0.3554	-0.0713	0.1399	0.2139	-0.288	0.0915	0.2364	-0.0471	0.0272	-0.0237	-0.0171	-0.2093	64.2354	99.14	62.7788
4	15.239	-5.4731	7.2411	12.2884	-23.0304	61.4692	0.2461	0.0053	-0.6162	-0.5339	0.7418	0.5046	1.5328	-2.9983	-0.9879	0.3483	-0.2998	0.0052	-0.0037	0.0051	0.1479	52.1025	84.3319	56.6151
5	1.9676	-0.1447	-0.2942	3.5117	-1.1424	2.3063	-0.0172	0.142	0.0106	0.2661	0.1661	0.6189	0.3363	-0.5103	-0.1489	-0.0518	-0.1369	0.0781	-0.0015	-0.0174	-0.0312	52.1275	101.174	43.2186
6	1.3037	0.1604	0.1594	4.9737	-1.0095	1.4697	0.0396	-0.0042	0.3373	0.3288	0.0586	0.2905	0.0432	-0.2292	-0.0981	-0.1874	-0.0382	0.0513	-0.0122	-0.0131	-0.0774	57.3489	113.5643	41.4598
7	21.7403	1.1992	12.5816	21.3881	19.1793	23.3073	-0.5744	-1.2691	1.8735	0.0461	-0.485	0.9327	-3.3832	-0.7385	1.0594	0.4176	0.0761	-0.0198	-0.1853	-0.0183	-0.0463	65.0066	118.5349	58.8934
8	1.0958	-0.3904	0.2492	1.7639	-0.849	1.8507	-0.0302	-0.011	0.0894	0.2559	-0.1034	-0.0951	0.2703	0.0219	0.1335	-0.0164	-0.0438	0.0325	-0.1255	-0.0198	-0.197	68.2386	104.1665	50.9949
9	2.8484	3.0585	-1.0614	3.2918	-1.2441	1.787	0.2188	-0.2319	0.3243	1.1001	-0.0919	0.0276	-0.3858	-0.1487	-0.1269	-0.1239	0.0167	0.0253	-0.1594	-0.0017	0.0523	84.5368	126.0519	55.2542
10	10.3975	-2.6726	0.2301	3.413	0.7701	3.0889	-0.2259	-0.1558	0.8013	0.1359	0.1958	-0.4553	-0.4007	0.1434	0.0301	-0.1521	-0.1033	-0.0304	-0.1562	-0.0458	0.2023	96.4091	133.7844	43.7302
11	2.5791	1.821	-0.7726	4.767	0.4904	1.9096	0.0701	0.0261	0.0076	0.2551	0.0175	-0.6544	-0.0463	0.4344	-0.0876	-0.2151	-0.0131	-0.0821	0.0288	0.0108	0.2343	101.9659	124.7312	41.0198
12	2.9138	1.4696	-0.0902	7.8535	-1.1637	2.7428	-0.0206	0.3276	-0.0798	-0.1137	0.0652	-0.7484	0.1272	0.3094	-0.0446	-0.2175	0.0453	-0.0255	0.1436	0.0138	0.2584	101.4917	122.8953	36.117
13	1.1011	-0.9671	1.1991	8.5116	-3.0509	2.4888	0.0561	0.2807	0.1272	-0.1786	-0.1299	-0.4845	-0.094	0.2088	0.0738	-0.1988	-0.0008	-0.0015	-0.0393	0.0588	0.1096	91.9849	126.8604	35.0788
14	2.2496	0.9696	0.045	4.4959	0.2652	2.1053	-0.2206	0.5299	0.3648	-0.6926	0.1598	-0.1826	-0.0659	-0.1517	0.0608	-0.0955	-0.0304	0.0277	0.0266	0.1284	-0.0898	74.0272	121.7259	22.8501
15	0.9024	0.9126	-0.0264	4.381	0.029	2.288	-0.1039	0.2239	0.0461	-0.2401	-0.0706	-0.2622	0.339	-0.0795	0.1745	-0.1443	-0.0249	0.0444	-0.0169	0.0212	-0.1795	72.4373	109.7879	28.1511
16	49.2872	-15.2476	13.5386	14.9798	-5.8831	17.2736	0.6836	2.1025	-4.4185	-0.7016	-0.2095	-0.3847	1.6845	1.1949	-0.4741	-0.0935	0.0037	-0.0641	-0.1401	-0.1841	0.309	88.8693	104.7012	37.3823
17	2.0783	1.0826	0.2499	1.8759	0.6984	1.1137	0.0447	-0.0315	0.1199	0.2335	-0.075	-0.1263	0.1665	0.0329	0.0303	-0.2074	0.009	-0.0211	-0.1233	0.033	-0.0969	80.8652	118.7432	40.5024
18	7.9371	5.6815	-1.3305	5.1774	-2.4815	2.3287	-0.6035	0.3652	-1.8673	-0.0839	0.4465	-1.9043	0.527	0.2832	0.157	0.2427	-0.0576	0.1508	-0.2019	-0.0426	0.0915	80.4227	93.1391	56.4518
19	186.497	41.6152	-20.5483	36.7867	-16.2262	7.1917	2.8695	-1.2722	-2.184	2.2623	-3.3671	-0.6417	2.0695	-1.7364	0.4977	0.003	0.005	0.0025	-0.0012	0.0027	-0.001	102.9408	88.8971	74.795
20	5.43	-3.3198	1.6016	3.1556	-2.7772	3.3436	-0.8479	0.3083	-0.2073	-0.1931	-0.6671	0.3845	0.2031	1.2656	1.515	-0.1089	0.0129	0.2465	0.0272	-0.0282	-0.0652	90.6382	89.6459	63.2552
21	39.8504	14.0728	5.7501	8.26	-0.7933	3.2533	-1.3253	-0.9779	-0.5013	-0.3123	-0.1398	-0.5896	0.4089	0.1045	1.4651	-0.1103	0.1818	0.1165	-0.4969	0.1235	-0.2695	84.887	90.7214	62.2867
22	5.6181	4.7688	2.2873	12.9191	0.1098	1.3094	0.5433	-0.8213	-0.7346	0.8026	-2.0519	-0.6948	0.2688	-0.3307	1.5087	0.0396	0.1095	0.093	0.0264	0.0581	0.0193	96.3471	86.0684	63.8504
23	32.1918	4.1927	-13.5698	9.8	-9.6673	12.4642	0.6728	-1.8738	0.6061	2.8186	-0.1628	-0.1411	-0.1066	1.0926	-0.5101	-0.0043	-0.0005	-0.0051	0.0016	0	-0.0006	101.9186	90.5081	69.8656
24	5.2415	-0.1856	0.4804	4.2643	0.7432	15.5321	0.1025	-0.4358	-0.1149	0.714	0.0554	-0.4388	0.6893	-1.0203	-0.1579	-0.1259	-0.0477	-0.0643	-0.4093	-0.1401	-0.3897	90.7444	132.9329	63.662
25	3.4148	1.8571	2.7402	7.1441	-5.2811	24.2094	0.4989	-0.3502	0.342	0.8996	-0.3728	0.1333	0.5512	0.0279	-0.1261	-0.305	0.0034	-0.0551	-0.4608	-0.1294	-0.2338	90.2929	132.4538	57.6331
26	0.4862	1.2899	1.8684	3.7601	6.6364	15.5301	0.539	-1.6132	0.6393	0.6526	-0.2313	-1.2757	1.2634	-0.8339	-0.3078	0.0192	-0.0686	0.0526	0.0104	0.0091	-0.0019	90.8389	136.944	68.6529
27	1.5018	4.8662	-0.3836	18.5969	-3.2748	1.5573	-0.1824	-1.075	0.0948	0.9952	-0.8291	-3.4664	-0.1077	1.7367	1.0114	0.0008	-0.0006	0.002	-0.0024	-0.0072	-0.0013	96.5253	135.0892	72.1612

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	12 - 94	12 - 94
2	X-RAY DIFFRACTION	2	A	A	95 - 150	95 - 150
3	X-RAY DIFFRACTION	3	A	A	151 - 175	151 - 175
4	X-RAY DIFFRACTION	4	A	A	176 - 188	176 - 188
5	X-RAY DIFFRACTION	5	A	A	189 - 249	189 - 249
6	X-RAY DIFFRACTION	6	A	A	250 - 303	250 - 303
7	X-RAY DIFFRACTION	7	A	A	304 - 312	304 - 312
8	X-RAY DIFFRACTION	8	A	A	327 - 379	327 - 379
9	X-RAY DIFFRACTION	9	A	A	380 - 402	380 - 402
10	X-RAY DIFFRACTION	10	B	B	12 - 43	12 - 43
11	X-RAY DIFFRACTION	11	B	B	44 - 94	44 - 94
12	X-RAY DIFFRACTION	12	B	B	95 - 151	95 - 151
13	X-RAY DIFFRACTION	13	B	B	152 - 190	152 - 190
14	X-RAY DIFFRACTION	14	B	B	191 - 247	191 - 247
15	X-RAY DIFFRACTION	15	B	B	248 - 303	248 - 303
16	X-RAY DIFFRACTION	16	B	B	304 - 312	304 - 312
17	X-RAY DIFFRACTION	17	B	B	327 - 380	327 - 380
18	X-RAY DIFFRACTION	18	B	B	381 - 404	381 - 404
19	X-RAY DIFFRACTION	19	C	C	128 - 136	1 - 9
20	X-RAY DIFFRACTION	20	C	C	137 - 162	10 - 35
21	X-RAY DIFFRACTION	21	C	C	163 - 181	36 - 54
22	X-RAY DIFFRACTION	22	C	C	182 - 199	55 - 72
23	X-RAY DIFFRACTION	23	C	C	200 - 214	73 - 87
24	X-RAY DIFFRACTION	24	D	D	137 - 163	10 - 36
25	X-RAY DIFFRACTION	25	D	D	164 - 181	37 - 54
26	X-RAY DIFFRACTION	26	D	D	182 - 200	55 - 73
27	X-RAY DIFFRACTION	27	D	D	201 - 209	74 - 82

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Yorodumi