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- PDB-3rnm: The crystal structure of the subunit binding of human dihydrolipo... -

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Basic information

Entry
Database: PDB / ID: 3rnm
TitleThe crystal structure of the subunit binding of human dihydrolipoamide transacylase (E2b) bound to human dihydrolipoamide dehydrogenase (E3)
Components
  • Dihydrolipoyl dehydrogenase, mitochondrial
  • Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial
KeywordsOXIDOREDUCTASE/PROTEIN BINDING / protein-protein interaction / redox protein / mitochondrion / OXIDOREDUCTASE-PROTEIN BINDING complex
Function / homology
Function and homology information


dihydrolipoyllysine-residue (2-methylpropanoyl)transferase / dihydrolipoamide branched chain acyltransferase activity / acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / OADH complex synthesizes glutaryl-CoA from 2-OA / Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD / oxoadipate dehydrogenase complex / Glycine degradation / branched-chain alpha-ketoacid dehydrogenase complex ...dihydrolipoyllysine-residue (2-methylpropanoyl)transferase / dihydrolipoamide branched chain acyltransferase activity / acetyltransferase complex / acrosomal matrix / OGDH complex synthesizes succinyl-CoA from 2-OG / OADH complex synthesizes glutaryl-CoA from 2-OA / Loss-of-function mutations in BCKDHA or BCKDHB cause MSUD / oxoadipate dehydrogenase complex / Glycine degradation / branched-chain alpha-ketoacid dehydrogenase complex / BCKDH synthesizes BCAA-CoA from KIC, KMVA, KIV / Loss-of-function mutations in DBT cause MSUD2 / Loss-of-function mutations in DLD cause MSUD3/DLDD / H139Hfs13* PPM1K causes a mild variant of MSUD / PDH complex synthesizes acetyl-CoA from PYR / Branched-chain ketoacid dehydrogenase kinase deficiency / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / lipoic acid binding / Regulation of pyruvate dehydrogenase (PDH) complex / Protein lipoylation / pyruvate decarboxylation to acetyl-CoA / oxoglutarate dehydrogenase complex / pyruvate dehydrogenase complex / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / 2-oxoglutarate metabolic process / pyruvate metabolic process / Signaling by Retinoic Acid / motile cilium / acyltransferase activity, transferring groups other than amino-acyl groups / sperm capacitation / acetyltransferase activity / mitochondrial nucleoid / RHOH GTPase cycle / mitochondrial electron transport, NADH to ubiquinone / gastrulation / Mitochondrial protein degradation / regulation of membrane potential / flavin adenine dinucleotide binding / microtubule cytoskeleton / mitochondrial matrix / ubiquitin protein ligase binding / mitochondrion / proteolysis / nucleus / cytosol / cytoplasm
Similarity search - Function
E3-binding domain / Dihydrolipoamide Transferase / Dihydrolipoamide dehydrogenase / : / : / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site ...E3-binding domain / Dihydrolipoamide Transferase / Dihydrolipoamide dehydrogenase / : / : / 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) / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / FAD/NAD-linked reductase, dimerisation domain superfamily / Chloramphenicol acetyltransferase-like domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase, mitochondrial / Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsBrautigam, C.A. / Wynn, R.M. / Chuang, J.C. / Young, B.B. / Chuang, D.T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Thermodynamic Basis for Weak Interactions between Dihydrolipoamide Dehydrogenase and Subunit-binding Domain of the Branched-chain {alpha}-Ketoacid Dehydrogenase Complex.
Authors: Brautigam, C.A. / Wynn, R.M. / Chuang, J.L. / Naik, M.T. / Young, B.B. / Huang, T.H. / Chuang, D.T.
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrolipoyl dehydrogenase, mitochondrial
B: Dihydrolipoyl dehydrogenase, mitochondrial
C: Dihydrolipoyl dehydrogenase, mitochondrial
D: Dihydrolipoyl dehydrogenase, mitochondrial
E: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial
F: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,07718
Polymers223,7946
Non-polymers4,28412
Water6,251347
1
A: Dihydrolipoyl dehydrogenase, mitochondrial
B: Dihydrolipoyl dehydrogenase, mitochondrial
E: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0399
Polymers111,8973
Non-polymers2,1426
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Dihydrolipoyl dehydrogenase, mitochondrial
D: Dihydrolipoyl dehydrogenase, mitochondrial
F: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,0399
Polymers111,8973
Non-polymers2,1426
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.136, 112.308, 122.545
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChains A, B, and E / Chains C, D, and F

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein
Dihydrolipoyl dehydrogenase, mitochondrial / Dihydrolipoamide dehydrogenase / Glycine cleavage system L protein


Mass: 52652.137 Da / Num. of mol.: 4 / Fragment: Residues 36-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLD, GCSL, LAD, PHE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P09622, dihydrolipoyl dehydrogenase
#2: Protein Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial / Branched-chain alpha-keto acid dehydrogenase complex component E2 / BCKAD-E2 / BCKADE2 / ...Branched-chain alpha-keto acid dehydrogenase complex component E2 / BCKAD-E2 / BCKADE2 / Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex / Dihydrolipoamide branched chain transacylase / Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase


Mass: 6592.526 Da / Num. of mol.: 2 / Fragment: subunit-binding domain, residues 165-213 / Mutation: R118N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DBT, BCATE2 / Production host: Escherichia coli (E. coli)
References: UniProt: P11182, dihydrolipoyllysine-residue (2-methylpropanoyl)transferase

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Non-polymers , 4 types, 359 molecules

#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 18% PEG3350 0.1 M CHES , pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 88688 / Num. obs: 88688 / % possible obs: 100 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.44 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→44.872 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 4446 5.02 %random
Rwork0.1814 ---
obs0.1843 88635 99.28 %-
all-88635 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.59 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.8722 Å20 Å2-2.7522 Å2
2--8.26 Å20 Å2
3----1.3878 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14720 0 280 347 15347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815262
X-RAY DIFFRACTIONf_angle_d1.08220639
X-RAY DIFFRACTIONf_dihedral_angle_d13.775615
X-RAY DIFFRACTIONf_chiral_restr0.0682378
X-RAY DIFFRACTIONf_plane_restr0.0042622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42550.38871230.30162222X-RAY DIFFRACTION80
2.4255-2.4540.35061330.26992816X-RAY DIFFRACTION100
2.454-2.48390.29961400.25752863X-RAY DIFFRACTION100
2.4839-2.51540.32231500.25542783X-RAY DIFFRACTION100
2.5154-2.54850.30911560.23742857X-RAY DIFFRACTION100
2.5485-2.58340.3221420.23512768X-RAY DIFFRACTION100
2.5834-2.62030.29121490.23662807X-RAY DIFFRACTION100
2.6203-2.65940.34321460.22522819X-RAY DIFFRACTION100
2.6594-2.70090.31421310.21182838X-RAY DIFFRACTION100
2.7009-2.74520.27051540.20882811X-RAY DIFFRACTION100
2.7452-2.79250.30631610.21222815X-RAY DIFFRACTION100
2.7925-2.84330.26451620.2142816X-RAY DIFFRACTION100
2.8433-2.8980.29181590.20642801X-RAY DIFFRACTION100
2.898-2.95710.32161420.20452808X-RAY DIFFRACTION100
2.9571-3.02140.2861420.20852859X-RAY DIFFRACTION100
3.0214-3.09170.25691440.19252776X-RAY DIFFRACTION100
3.0917-3.1690.24841420.20022823X-RAY DIFFRACTION100
3.169-3.25460.2551440.20362878X-RAY DIFFRACTION100
3.2546-3.35040.28041440.19542821X-RAY DIFFRACTION100
3.3504-3.45850.24451310.20362820X-RAY DIFFRACTION100
3.4585-3.58210.25841670.19772818X-RAY DIFFRACTION100
3.5821-3.72540.27241540.19622819X-RAY DIFFRACTION100
3.7254-3.89490.25231500.17912838X-RAY DIFFRACTION100
3.8949-4.10010.20661270.15362835X-RAY DIFFRACTION100
4.1001-4.35680.17281480.13372839X-RAY DIFFRACTION100
4.3568-4.69280.18541730.12212840X-RAY DIFFRACTION100
4.6928-5.16450.16611450.13082823X-RAY DIFFRACTION100
5.1645-5.91030.20031410.16222864X-RAY DIFFRACTION100
5.9103-7.44090.20341700.16672841X-RAY DIFFRACTION100
7.4409-44.87980.18831760.15142871X-RAY DIFFRACTION99
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)
10.29440.117-0.06630.28630.07390.26970.0078-0.03310.0182-0.0078-0.08460.053-0.0589-0.01120.0520.06210.0097-0.00270.0642-0.00850.0459-18.03472.897631.3639
20.04270.03150.01110.1049-0.1170.2317-0.00640.0214-0.0134-0.0078-0.1384-0.1758-0.02750.28140.1340.0864-0.02140.01610.31970.15290.18416.61137.489624.4501
30.3977-0.17130.1980.2118-0.09550.31020.04120.04210.072-0.01440.0033-0.05620.06160.0204-0.01960.1020.0387-0.00390.07760.01980.089-21.115-50.412439.0791
40.4045-0.08020.31980.3556-0.03430.25430.056-0.061-0.0049-0.0679-0.05360.0860.0252-0.1038-0.00450.09630.0256-0.0330.14250.02990.0812-55.7099-49.306230.3869
50.74260.4267-0.26350.64840.46711.04150.05740.00530.06950.0850.0606-0.23910.08070.0173-0.11470.1875-0.00890.01060.166-0.00930.2412-4.073641.506831.5875
60.13740.0051-0.00250.0440.08820.17780.00010.06080.0715-0.4072-0.0987-0.0671-0.1931-0.03560.09830.6940.0354-0.05330.52710.02390.7117-36.5924-83.335630.6687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B
3X-RAY DIFFRACTION3Chain C
4X-RAY DIFFRACTION4Chain D
5X-RAY DIFFRACTION5Chain E
6X-RAY DIFFRACTION6Chain F

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