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- PDB-6zzl: Crystal structure of the catalytic domain plus N-terminal linker ... -

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Basic information

Entry
Database: PDB / ID: 6zzl
TitleCrystal structure of the catalytic domain plus N-terminal linker of the acetyltransferase AceF (E2p) from Corynebacterium glutamicum.
ComponentsDihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
KeywordsTRANSFERASE / PDH / 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
PHOSPHATE ION / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.229 Å
AuthorsYang, L. / Bellinzoni, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE92-0003 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9786
Polymers99,6993
Non-polymers2793
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-78 kcal/mol
Surface area29820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.392, 170.392, 67.56
Angle α, β, γ (deg.)90, 90, 120
Int Tables number172
Space group name H-MP64

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Components

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


Mass: 33232.898 Da / Num. of mol.: 3
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.229→85.196 Å / Num. obs: 40013 / % possible obs: 95 % / Redundancy: 20.6 % / CC1/2: 0.999 / Rpim(I) all: 0.027 / Net I/σ(I): 16
Reflection shellResolution: 2.229→2.371 Å / Redundancy: 15.9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2001 / CC1/2: 0.629 / Rpim(I) all: 0.484 / % possible all: 74.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
autoPROCdata reduction
XDSJan 31, 202data reduction
autoPROC1.0.5data scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZZJ

6zzj


Resolution: 2.229→85.196 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.291 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.291 / SU Rfree Blow DPI: 0.202 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 2025 -RANDOM
Rwork0.1904 ---
obs0.1915 40013 72.9 %-
Displacement parametersBiso mean: 63.39 Å2
Baniso -1Baniso -2Baniso -3
1--3.269 Å20 Å20 Å2
2---3.269 Å20 Å2
3---6.5381 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.229→85.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5721 0 17 308 6046
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085829HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.967947HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2706SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes987HARMONIC5
X-RAY DIFFRACTIONt_it5829HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion842SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4752SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion2.33
LS refinement shellResolution: 2.23→2.31 Å
RfactorNum. reflection% reflection
Rfree0.2817 47 -
Rwork0.2268 --
obs0.2301 801 14.85 %
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)
11.90350.17580.02742.36760.79881.3127-0.11770.0697-0.08310.06970.1425-0.0702-0.0831-0.0702-0.0248-0.06860.0155-0.0171-0.22680.017-0.0137-77.04127.3336-18.67
21.65980.22110.19052.2580.33290.684-0.1415-0.23780.042-0.23780.21020.15880.0420.1588-0.0687-0.0605-0.06460.0479-0.1649-0.0714-0.0005-63.12866.1318-33.14
32.33720.77080.15132.30030.37741.278-0.1358-0.1357-0.1218-0.13570.25070.3112-0.12180.3112-0.115-0.1848-0.07530.014-0.235-0.10130.131-48.292230.0452-24.3076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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