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

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Basic information

Entry
Database: PDB / ID: 3crl
TitleCrystal structure of the PDHK2-L2 complex.
Components
  • Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrialDihydrolipoyl transacetylase
  • Pyruvate dehydrogenase [lipoamide] kinase isozyme 2, mitochondrial
KeywordsTRANSFERASE / 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 / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / pyruvate dehydrogenase complex / : ...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 / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / pyruvate dehydrogenase complex / : / regulation of cellular ketone metabolic process / Pyruvate metabolism / regulation of pH / cellular response to nutrient / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / regulation of gluconeogenesis / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of glucose metabolic process / regulation of calcium-mediated signaling / tricarboxylic acid cycle / cellular response to reactive oxygen species / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / peptidyl-serine phosphorylation / mitochondrial matrix / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / protein-containing complex binding / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding
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. ...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. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Chloramphenicol acetyltransferase-like domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial / [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 Å
AuthorsPopov, K.M. / Luo, M. / Green, T.J. / Grigorian, A. / Klyuyeva, A. / Tuganova, A.
CitationJournal: 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
DepositionApr 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,97910
Polymers111,8404
Non-polymers1,1396
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12450 Å2
ΔGint-64.5 kcal/mol
Surface area40800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.413, 121.630, 71.452
Angle α, β, γ (deg.)90.000, 97.290, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12C
22D

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERLEUAA12 - 16812 - 168
211SERLEUBB12 - 16812 - 168
321SERPHEAA179 - 340179 - 340
421SERPHEBB179 - 340179 - 340
112HISILECC132 - 2145 - 87
212HISHOHDD - N132 - 2165 - 2

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

#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

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Non-polymers , 4 types, 148 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→70.89 Å / Num. obs: 32860 / % possible obs: 90.6 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.3
Reflection shellResolution: 2.61→2.9 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.73 / % possible all: 64.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.893 / SU B: 24.813 / SU ML: 0.275 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.287 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1641 5 %RANDOM
Rwork0.2205 ---
obs0.223 32859 89.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.13 Å2
2--1.97 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7459 0 66 142 7667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227702
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.9910466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5075932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93524.478335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.619151310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7791536
X-RAY DIFFRACTIONr_chiral_restr0.0680.21169
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025766
X-RAY DIFFRACTIONr_nbd_refined0.2020.23694
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25157
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2335
X-RAY DIFFRACTIONr_metal_ion_refined0.2220.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.27
X-RAY DIFFRACTIONr_mcbond_it0.3551.54698
X-RAY DIFFRACTIONr_mcangle_it0.65227641
X-RAY DIFFRACTIONr_scbond_it0.7233049
X-RAY DIFFRACTIONr_scangle_it1.1874.52825
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2468MEDIUM POSITIONAL0.370.5
1A2468MEDIUM THERMAL0.212
2C648MEDIUM POSITIONAL0.330.5
2C648MEDIUM THERMAL0.082
LS refinement shellResolution: 2.61→2.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 63 -
Rwork0.302 1374 -
all-1437 -
obs--53.78 %
Refinement TLS params.

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

IDL11 (°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)
12.0985-0.6152-0.38852.404-0.02373.0643-0.10590.0658-0.36930.27560.0735-0.1820.74570.45590.03240.4029-0.02010.0660.01250.02150.018567.320388.380566.8343
22.0080.9539-0.10464.8199-0.59963.50460.0129-0.15680.0840.8406-0.1119-0.0522-0.2204-0.18370.0990.3682-0.06890.06420.1529-0.0354-0.105363.1762101.236772.1438
30.07940.39060.38235.7788-0.44863.2463-0.03710.11530.02930.73040.10020.48250.3004-0.4944-0.06320.305-0.17490.16570.2717-0.04730.049957.639594.978860.81
41.02210.1978-0.0884.9917-1.06942.6467-0.06460.3741-0.18060.22430.01880.91290.4949-0.47960.0458-0.0193-0.12050.07020.24-0.04950.193349.9828102.589741.1157
51.32240.37790.29095.5721-1.20171.2342-0.02170.10720.24210.20780.1290.56420.1361-0.1838-0.1074-0.0118-0.03650.08540.243-0.0220.158555.6433111.167242.4188
69.04871.1446-1.46612.5724-5.07410.0818-0.3203-0.35431.77271.45470.35180.0584-2.8403-0.1142-0.03150.8295-0.00450.00590.1622-0.09190.082464.3913119.744956.14
70.9021-1.2961-0.54516.579-1.34531.4-0.049-0.02570.2050.3101-0.08490.07350.05920.20970.13390.1293-0.05760.0220.1949-0.0490.105862.4387109.613447.9597
83.92852.7926.52543.8474.321911.9451-0.16520.3332-0.2327-0.00390.2811-0.50970.02320.7874-0.1160.2405-0.00810.06730.16260.04890.077375.060899.250759.0297
90.75121.12270.63411.79331.0640.65240.1904-0.46480.37130.9542-0.29370.0219-0.1654-0.19370.10340.2355-0.00630.07010.21850.01910.35283.479129.465654.1287
103.1140.98320.13772.27430.36961.55240.02870.02450.29020.2111-0.059-0.5039-0.20550.26590.0304-0.1045-0.01240.00690.13510.05250.4084100.3653131.962340.2559
110.75071.17770.41459.6165-1.14674.27030.0080.2756-0.47990.29740.1666-0.99930.64960.0518-0.1746-0.08190.0664-0.03770.15110.03740.530997.7231111.813337.111
123.6821-1.38571.66774.7379-1.56490.96370.12350.40510.3515-0.6068-0.2415-0.43330.11430.38640.1180.0245-0.00140.08710.19110.12760.34390.8062129.333532.2801
131.73991.6762-0.35135.34120.08121.2608-0.17340.4430.2875-1.04450.1194-0.1483-0.1524-0.24470.0540.1642-0.01970.06440.27830.12430.078272.0098122.28921.716
141.04341.51560.72254.8616-0.65481.5921-0.20390.25790.0546-0.49690.1281-0.14370.21210.05450.07580.0485-0.01940.09760.26360.02120.113172.6917113.654527.5442
1527.29250.3254.14963.5367-4.22185.79490.89310.5869-2.35340.2081-0.305-1.38732.1239-0.2586-0.58810.04260.0208-0.01770.1184-0.05710.641385.0699105.040337.9269
161.54750.44130.12235.32142.32974.1475-0.1083-0.0688-0.13140.02170.2131-0.62760.25650.0712-0.1048-0.01480.0060.03940.19220.03220.305583.327117.408634.8439
171.94211.21550.46582.1421.17981.33520.14510.01920.26960.1799-0.13520.04030.1848-0.1145-0.00990.04160.02070.04360.19080.01210.21176.7086120.033139.9718
182.94890.3929-1.0030.3909-0.7311.3951-0.05710.347-0.69990.6810.0294-0.63770.05150.3910.02770.2377-0.0580.05020.14520.04720.198881.525797.799456.5615
1932.8002-11.306-6.19813.89712.13641.1712-0.29990.26892.73112.15270.49581.1804-0.64430.1244-0.19580.73390.4532-0.29580.63260.4030.5699101.398389.96775.1311
209.69281.0608-0.29840.5395-1.46674.866-0.52180.7458-0.6225-0.0599-0.3112-0.42540.09060.50650.8330.20640.09740.12770.20820.20680.234289.251690.479663.4017
2130.95639.46422.3023.8-1.62296.1429-1.377-0.82050.3464-0.9279-0.42840.0177-0.01290.51551.80540.21330.12490.0288-0.040.07660.30684.947892.3862.6109
2215.6334-3.51372.60946.2477-1.37210.54860.14560.4716-0.55160.7642-0.1395-0.0477-0.43380.4061-0.00610.35950.29050.17090.2470.25350.133794.890487.157663.7481
2310.3208-4.0516-6.83141.59052.68184.5217-0.72511.7262-0.52141.64121.37311.9455-1.33060.5081-0.6480.9420.12270.19120.74510.60920.8148100.598591.811369.6485
241.67293.1493-2.598111.5327-16.138726.60980.0425-0.81930.28831.202-0.4083-0.24292.0567-1.96510.36570.5387-0.0178-0.1620.57620.05530.3464100.8891135.091577.6636
254.85260.81880.46135.4827-0.1519.1010.3966-0.9430.18950.4296-0.34970.52510.7466-0.6488-0.04680.3183-0.0126-0.05490.1048-0.1680.028789.6148134.025163.5149
263.61874.55031.37316.6224-1.904715.160.8593-0.35550.46961.4041-0.51840.2740.5444-0.2667-0.3410.225-0.0930.00460.0626-0.20380.046189.2387132.691558.9543
279.4834-5.1813-1.263316.0513-1.640811.23150.2626-0.94660.08571.7895-0.4852-0.10930.0286-0.56950.22260.0824-0.290.11610.0224-0.25630.106489.7562137.972368.5764
2810.763-4.1328-0.23351.58690.08970.0051-1.7231-1.6089-0.9135-1.42-0.0245-1.35980.48270.59431.74770.691-0.09560.05810.60810.09970.666594.7652132.565576.4863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 4912 - 49
2X-RAY DIFFRACTION2AA50 - 15150 - 151
3X-RAY DIFFRACTION3AA152 - 188152 - 188
4X-RAY DIFFRACTION4AA189 - 238189 - 238
5X-RAY DIFFRACTION5AA239 - 299239 - 299
6X-RAY DIFFRACTION6AA300 - 312300 - 312
7X-RAY DIFFRACTION7AA323 - 361323 - 361
8X-RAY DIFFRACTION8AA362 - 381362 - 381
9X-RAY DIFFRACTION9AA382 - 402382 - 402
10X-RAY DIFFRACTION10BB12 - 11612 - 116
11X-RAY DIFFRACTION11BB117 - 150117 - 150
12X-RAY DIFFRACTION12BB151 - 188151 - 188
13X-RAY DIFFRACTION13BB189 - 238189 - 238
14X-RAY DIFFRACTION14BB239 - 299239 - 299
15X-RAY DIFFRACTION15BB300 - 312300 - 312
16X-RAY DIFFRACTION16BB323 - 343323 - 343
17X-RAY DIFFRACTION17BB344 - 376344 - 376
18X-RAY DIFFRACTION18BB377 - 404377 - 404
19X-RAY DIFFRACTION19CC128 - 1361 - 9
20X-RAY DIFFRACTION20CC137 - 16210 - 35
21X-RAY DIFFRACTION21CC163 - 18136 - 54
22X-RAY DIFFRACTION22CC182 - 19955 - 72
23X-RAY DIFFRACTION23CC200 - 21473 - 87
24X-RAY DIFFRACTION24DD128 - 1361 - 9
25X-RAY DIFFRACTION25DD137 - 16310 - 36
26X-RAY DIFFRACTION26DD164 - 18137 - 54
27X-RAY DIFFRACTION27DD182 - 20055 - 73
28X-RAY DIFFRACTION28DD201 - 21474 - 87

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