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- PDB-6zzi: Crystal structure of the catalyic domain of Corynebacterium gluta... -

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Basic information

Entry
Database: PDB / ID: 6zzi
TitleCrystal structure of the catalyic domain of Corynebacterium glutamicum acetyltransferase AceF (E2p).
ComponentsDihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complexDihydrolipoyl transacetylase
KeywordsTRANSFERASE / PDH / ODH / acetyltransferase / lipoamide / corynebacterium / CoA
Function / homology
Function and homology information


dihydrolipoyllysine-residue succinyltransferase activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / tricarboxylic acid cycle / cytosol
Similarity search - Function
2-oxoglutarate dehydrogenase, E2 component / 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 ...2-oxoglutarate dehydrogenase, E2 component / 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
Similarity search - Domain/homology
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.932 Å
AuthorsBruch, E.M. / Lexa-Sapart, N. / Bellinzoni, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-13-JSV8-0003 France
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Actinobacteria challenge the paradigm: A unique protein architecture for a well-known, central metabolic complex.
Authors: Eduardo M Bruch / Pierre Vilela / Lu Yang / Alexandra Boyko / Norik Lexa-Sapart / Bertrand Raynal / Pedro M Alzari / Marco Bellinzoni /
Abstract: α-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, ...α-oxoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have been, so far, all considered to be structured around a high-molecular weight hollow core, consisting of up to 60 subunits of the acyltransferase component. We provide here evidence that Actinobacteria break the rule by possessing an acetyltranferase component reduced to its minimally active, trimeric unit, characterized by a unique C-terminal helix bearing an actinobacterial specific insertion that precludes larger protein oligomerization. This particular feature, together with the presence of an gene coding for both the decarboxylase and the acyltransferase domains on the same polypetide, is spread over Actinobacteria and reflects the association of PDH and ODH into a single physical complex. Considering the central role of the pyruvate and 2-oxoglutarate nodes in central metabolism, our findings pave the way to both therapeutic and metabolic engineering applications.
History
DepositionAug 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 15, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
C: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
D: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
E: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
F: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex


Theoretical massNumber of molelcules
Total (without water)156,9726
Polymers156,9726
Non-polymers00
Water22,6451257
1
A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
C: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex


Theoretical massNumber of molelcules
Total (without water)78,4863
Polymers78,4863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9500 Å2
ΔGint-47 kcal/mol
Surface area29340 Å2
MethodPISA
2
D: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
E: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
F: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex


Theoretical massNumber of molelcules
Total (without water)78,4863
Polymers78,4863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-45 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.278, 158.278, 63.016
Angle α, β, γ (deg.)90, 90, 120
Int Tables number143
Space group name H-MP3

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Components

#1: Protein
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoyl transacetylase / Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex / Pyruvate ...Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex / Pyruvate dehydrogenase complex component E2 / PDH component E2


Mass: 26161.945 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: aceF, sucB, Cgl2207, cg2421 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8NNJ2, dihydrolipoyllysine-residue acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1257 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes-Na pH 7.5, 5% PEG4000, 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.932→79.139 Å / Num. obs: 131357 / % possible obs: 99.3 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rpim(I) all: 0.043 / Net I/σ(I): 14
Reflection shellResolution: 1.932→1.966 Å / Num. unique obs: 6564 / CC1/2: 0.736 / Rpim(I) all: 0.369

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N72

4n72


Resolution: 1.932→79.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.124 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.109
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 6556 -RANDOM
Rwork0.1663 ---
obs0.1672 131357 99.2 %-
Displacement parametersBiso mean: 30.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.9813 Å20 Å20 Å2
2---0.9813 Å20 Å2
3---1.9626 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.932→79.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10944 0 0 1257 12201
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811153HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9115172HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5270SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1894HARMONIC5
X-RAY DIFFRACTIONt_it11153HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1596SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact10644SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion2.24
LS refinement shellResolution: 1.932→1.95 Å
RfactorNum. reflection% reflection
Rfree0.2726 131 -
Rwork0.2175 --
obs--96.39 %
Refinement TLS params.

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)
10.941-0.00080.1590.5329-0.02050.63710.038-0.02680.1779-0.02680.03010.08510.17790.0851-0.0681-0.03070.0076-0.0018-0.0816-0.0033-0.035325.277545.504114.2345
21.06690.396-0.13610.9516-0.06580.69530.01160.1046-0.09550.1046-0.01810.166-0.09550.1660.0064-0.0585-0.018-0.0074-0.0122-0.0462-0.081225.267574.439923.6514
31.20140.16940.03290.45040.10280.83080.005-0.094-0.138-0.0940.0332-0.0345-0.138-0.0345-0.0382-0.0056-0.01170.0152-0.07590.0046-0.04715.696365.49882.2723
40.41620.0877-0.03772.7273-0.20370.62890.03020.0653-0.10320.0653-0.0830.1633-0.10320.16330.0528-0.1458-0.0089-0.0188-0.12860.02180.105752.6436-0.4326-17.5284
50.8219-0.20750.09621.87330.20420.94870.00660.2452-0.1780.2452-0.0771-0.1208-0.178-0.12080.0704-0.02690.0270.0002-0.1091-0.0428-0.053826.829511.4085-6.8216
60.61960.2316-0.16891.19960.0641.17070.0176-0.1006-0.0396-0.1006-0.0109-0.1841-0.0396-0.1841-0.0067-0.06720.0318-0.0079-0.0376-0.0042-0.056626.2651-9.9754-28.4912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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