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- PDB-2ii4: Crystal structure of a cubic core of the dihydrolipoamide acyltra... -

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Basic information

Entry
Database: PDB / ID: 2ii4
TitleCrystal structure of a cubic core of the dihydrolipoamide acyltransferase (E2b) component in the branched-chain alpha-ketoacid dehydrogenase complex (BCKDC), Coenzyme A-bound form
ComponentsLipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
KeywordsTRANSFERASE / cubic core / homo trimer / CoA-bound form
Function / homology
Function and homology information


Branched-chain amino acid catabolism / RHOH GTPase cycle / Glyoxylate metabolism and glycine degradation / dihydrolipoyllysine-residue (2-methylpropanoyl)transferase / dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity / lipoic acid binding / carboxylic acid metabolic process / acetyltransferase activity / mitochondrial matrix / mitochondrion / cytoplasm
Similarity search - Function
Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / 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) ...Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / 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 / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.59 Å
AuthorsKato, M. / Wynn, R.M. / Chuang, J.L. / Brautigam, C.A. / Custorio, M. / Chuang, D.T.
CitationJournal: Embo J. / Year: 2006
Title: A synchronized substrate-gating mechanism revealed by cubic-core structure of the bovine branched-chain alpha-ketoacid dehydrogenase complex.
Authors: Kato, M. / Wynn, R.M. / Chuang, J.L. / Brautigam, C.A. / Custorio, M. / Chuang, D.T.
History
DepositionSep 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
B: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
C: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
D: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
E: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
F: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
G: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
H: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,37828
Polymers229,8138
Non-polymers6,56620
Water5,260292
1
A: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
B: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
C: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
D: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
E: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
F: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
G: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
H: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
hetero molecules

A: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
B: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
C: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
D: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
E: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
F: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
G: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
H: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
hetero molecules

A: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
B: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
C: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
D: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
E: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
F: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
G: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
H: Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)709,13584
Polymers689,43824
Non-polymers19,69760
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area131180 Å2
ΔGint-827 kcal/mol
Surface area212200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.234, 195.234, 172.756
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11G-810-

CL

21H-812-

CL

31H-842-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: 188 - 421 / Label seq-ID: 29 - 262

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
DetailsA biological functional unit of this protein is a 24-meric cubic core, containing 8 homo trimers. The asymmetric unit in this crystal with the R3 space group contains 8 monomers (two trimers and two monomers from two another trimers). It is too complex to describe the symmetry operations to generate the cubic core from the asymmetric unit. Therefore, we highly recommend to download the coordinates of the biological functional unit (the 24-meric cubic core) from the PDB web site.

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Components

#1: Protein
Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex / Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase / E2 / Dihydrolipoamide branched chain ...Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase / E2 / Dihydrolipoamide branched chain transacylase / BCKAD E2 subunit


Mass: 28726.576 Da / Num. of mol.: 8 / Fragment: core (catalytic) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: DBT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P11181, dihydrolipoyllysine-residue (2-methylpropanoyl)transferase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Na-acetate (pH 4.6), 28% PEG 4000, 0.15 M NH4-acetate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 75843 / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 / Χ2: 1.243 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.59-2.695.20.51976181.2531100
2.69-2.85.80.39375281.2921100
2.8-2.936.20.26976091.2881100
2.93-3.086.30.18975791.3181100
3.08-3.286.40.14575691.3241100
3.28-3.536.40.09276231.3421100
3.53-3.886.40.06575451.2241100
3.88-4.456.30.04976041.1711100
4.45-5.66.20.04775701.2311100
5.6-506.20.02775980.989199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.59→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 17.339 / SU ML: 0.192 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.515 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3805 5 %RANDOM
Rwork0.17 ---
obs0.173 75817 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.41 Å20 Å2
2---0.83 Å20 Å2
3---1.24 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14424 0 396 292 15112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02215096
X-RAY DIFFRACTIONr_angle_refined_deg1.9192.00720464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86151864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.85624.722576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.846152664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.461564
X-RAY DIFFRACTIONr_chiral_restr0.1220.22328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210920
X-RAY DIFFRACTIONr_nbd_refined0.2230.26589
X-RAY DIFFRACTIONr_nbtor_refined0.3250.210321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2724
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.234
X-RAY DIFFRACTIONr_mcbond_it1.2631.59545
X-RAY DIFFRACTIONr_mcangle_it1.621215000
X-RAY DIFFRACTIONr_scbond_it2.92336208
X-RAY DIFFRACTIONr_scangle_it4.2894.55464
Refine LS restraints NCS

Ens-ID: 1 / Number: 1803 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.375
2BLOOSE POSITIONAL0.365
3CLOOSE POSITIONAL0.435
4DLOOSE POSITIONAL0.445
5ELOOSE POSITIONAL0.395
6FLOOSE POSITIONAL0.485
7GLOOSE POSITIONAL0.435
8HLOOSE POSITIONAL0.395
1ALOOSE THERMAL2.5210
2BLOOSE THERMAL2.510
3CLOOSE THERMAL2.1910
4DLOOSE THERMAL2.6510
5ELOOSE THERMAL2.2610
6FLOOSE THERMAL2.6310
7GLOOSE THERMAL3.0810
8HLOOSE THERMAL2.7510
LS refinement shellResolution: 2.59→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 263 -
Rwork0.254 5172 -
obs-5435 97.8 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.36980.21950.02010.95520.21260.3931-0.0153-0.0613-0.01970.0583-0.0097-0.0479-0.07480.03650.0251-0.0295-0.0061-0.0143-0.0116-0.0067-0.0372chain a60.706-11.64-5.543
20.80540.2456-0.18860.6419-0.11910.35930.00280.0202-0.02720.0447-0.01250.03080.0622-0.02970.0097-0.0227-0.00770.0005-0.03950.0042-0.0192chain b45.115-35.626-14.007
30.4210.003-0.05560.44630.15950.8412-0.02240.0889-0.0474-0.08560.0507-0.0898-0.03580.0269-0.0284-0.021-0.00620.0355-0.0298-0.0192-0.0116chain c64.078-22.75-33.102
41.06510.1018-0.23220.43470.03570.4791-0.05440.0122-0.0496-0.00370.0236-0.04230.08390.09450.0309-0.02540.02020.0128-0.0127-0.0277-0.0158chain d24.881-61.869-41.772
50.67490.0728-0.06120.3016-0.19570.8944-0.0214-0.1129-0.12210.01720.04550.02820.01020.0068-0.0242-0.03830.02540.0302-0.05130.03330.0204chain e2.211-65.313-22.668
61.0012-0.12240.20440.7798-0.06120.3722-0.07090.1623-0.0415-0.07960.08170.0522-0.0061-0.0362-0.0107-0.0255-0.0453-0.0107-0.00020.0153-0.0174chain f-2.891-54.736-50.024
70.84840.22680.09461.25310.06850.2486-0.025-0.077-0.17990.0401-0.0853-0.01850.0164-0.01010.1103-0.03570.0140.0504-0.03670.04180.017chain g2.568-17.013.021
80.8067-0.22050.03370.797-0.01460.3454-0.0246-0.0265-0.11620.0380.0198-0.08860.0291-0.00420.0048-0.036-0.00550.0119-0.0440.0142-0.0018chain h9.733-14.184-58.278
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 188 - 421 / Label seq-ID: 29 - 262

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD
55EE
66FF
77GG
88HH

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