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- PDB-6zzk: Crystal structure of the catalytic domain of C. glutamicum AceF (... -

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Basic information

Entry
Database: PDB / ID: 6zzk
TitleCrystal structure of the catalytic domain of C. glutamicum AceF (E2p) in ternary complex with CoA and dihydrolipoamide.
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
COENZYME A / 6,8-DIMERCAPTO-OCTANOIC ACID AMIDE / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBruch, E.M. / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0665
Polymers52,3242
Non-polymers1,7423
Water5,765320
1
A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules

A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules

A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4119
Polymers78,4863
Non-polymers2,9256
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area15140 Å2
ΔGint-48 kcal/mol
Surface area28210 Å2
MethodPISA
2
B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules

B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules

B: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7886
Polymers78,4863
Non-polymers2,3033
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area13210 Å2
ΔGint-39 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.127, 132.127, 132.127
Angle α, β, γ (deg.)90, 90, 90
Int Tables number198
Space group name H-MP213

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: aceF, sucB, Cgl2207, cg2421 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8NNJ2, dihydrolipoyllysine-residue acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LPM / 6,8-DIMERCAPTO-OCTANOIC ACID AMIDE


Mass: 207.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NOS2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1 M Tris-HCl pH 7.3, 1.62 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.5498 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 2.09→93.43 Å / Num. obs: 45719 / % possible obs: 100 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rpim(I) all: 0.028 / Net I/σ(I): 16.6
Reflection shellResolution: 2.09→2.126 Å / Redundancy: 19.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2292 / CC1/2: 0.797 / Rpim(I) all: 0.334 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
autoPROCdata reduction
XDSNov 1, 2016data reduction
autoPROC1.0.5data scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZZJ

6zzj


Resolution: 2.09→93.43 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.172 2323 -RANDOM
Rwork0.1638 ---
obs0.1642 45719 100 %-
Displacement parametersBiso mean: 43.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.09→93.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3659 0 108 320 4087
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083834HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.915228HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1365SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes668HARMONIC5
X-RAY DIFFRACTIONt_it3834HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion545SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3161SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion13.3
LS refinement shellResolution: 2.09→2.1 Å
RfactorNum. reflection% reflection
Rfree0.2112 61 -
Rwork0.191 --
obs0.1923 915 100 %
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)
10.54390.16340.02431.2475-0.32511.11070.0314-0.0129-0.0955-0.0129-0.06150.2583-0.09550.25830.0301-0.0874-0.00680.0109-0.03530.0279-0.0608-46.23822.86560.2118
20.821-0.0035-0.12830.843-0.13080.9491-0.0287-0.03490.1897-0.03490.0365-0.14240.1897-0.1424-0.0078-0.0554-0.0343-0.01-0.0651-0.0046-0.0469-50.859426.6705-29.2926
30.58910.5421-0.33991.4438-0.67820.0045-0.00470.0079-0.17030.00790.0023-0.0183-0.1703-0.01830.0024-0.1080.07640.0296-0.0295-0.0734-0.0148-48.243915.9966-13.2605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|436 - A|675 }A436 - 675
2X-RAY DIFFRACTION2{ B|435 - B|675 }B435 - 675
3X-RAY DIFFRACTION3{ A|701 - A|702 B|701 - B|701 }A701 - 702
4X-RAY DIFFRACTION3{ A|701 - A|702 B|701 - B|701 }B701

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