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- PDB-6ysw: E. coli anaerobic trifunctional enzyme subunit-alpha in complex w... -

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Basic information

Entry
Database: PDB / ID: 6ysw
TitleE. coli anaerobic trifunctional enzyme subunit-alpha in complex with coenzyme A
ComponentsFatty acid oxidation complex subunit alphaBeta oxidation
KeywordsOXIDOREDUCTASE / fatty acid oxidation / lipid metabolism / hydratase / dehydrogenase / trifunctional enzyme / beta oxidation
Function / homology
Function and homology information


fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / cytoplasm
Similarity search - Function
Fatty oxidation complex, alpha subunit FadJ / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily ...Fatty oxidation complex, alpha subunit FadJ / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
COENZYME A / Fatty acid oxidation complex subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsSah-Teli, S.K. / Hynonen, M.J. / Wierenga, R.K. / Venkatesan, R.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland289024, 293369, 319194 Finland
Citation
Journal: Structure / Year: 2023
Title: Structural basis for different membrane-binding properties of E. coli anaerobic and human mitochondrial beta-oxidation trifunctional enzymes
Authors: Sah-Teli, S.K. / Pinkas, M. / Hynonen, M.J. / Butcher, S.J. / Wierenga, R.K. / Novacek, J. / Venkatesan, R.
#1: Journal: Biochem J / Year: 2019
Title: Complementary substrate specificity and distinct quaternary assembly of the aerobic and anaerobic β-oxidation trifunctional enzyme complexes.
Authors: Shiv K Sah-Teli / Mikko J Hynönen / Werner Schmitz / James A Geraets / Jani Seitsonen / Jan Skov Pedersen / Sarah J Butcher / Rik K Wierenga / Rajaram Venkatesan /
Abstract: The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in , EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions, ...The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in , EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions, whereas anEcTFE is expressed also under anaerobic conditions, with nitrate or fumarate as the ultimate electron acceptor. The anEcTFE subunits have higher sequence identity with the human mitochondrial TFE (HsTFE) than with the soluble EcTFE. Like HsTFE, here it is found that anEcTFE is a membrane-bound complex. Systematic enzyme kinetic studies show that anEcTFE has a preference for medium- and long-chain enoyl-CoAs, similar to HsTFE, whereas EcTFE prefers short chain enoyl-CoA substrates. The biophysical characterization of anEcTFE and EcTFE shows that EcTFE is heterotetrameric, whereas anEcTFE is purified as a complex of two heterotetrameric units, like HsTFE. The tetrameric assembly of anEcTFE resembles the HsTFE tetramer, although the arrangement of the two anEcTFE tetramers in the octamer is different from the HsTFE octamer. These studies demonstrate that EcTFE and anEcTFE have complementary substrate specificities, allowing for complete degradation of long-chain enoyl-CoAs under aerobic conditions. The new data agree with the notion that anEcTFE and HsTFE are evolutionary closely related, whereas EcTFE belongs to a separate subfamily.
History
DepositionApr 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 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
B: Fatty acid oxidation complex subunit alpha
A: Fatty acid oxidation complex subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,59216
Polymers157,5762
Non-polymers2,01614
Water34219
1
B: Fatty acid oxidation complex subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1725
Polymers78,7881
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fatty acid oxidation complex subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,42011
Polymers78,7881
Non-polymers1,63210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)204.793, 90.724, 128.625
Angle α, β, γ (deg.)90.000, 123.165, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-801-

SO4

21A-806-

SO4

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Components

#1: Protein Fatty acid oxidation complex subunit alpha / Beta oxidation


Mass: 78787.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal 6XHis-tag
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: fadJ, yfcX, b2341, JW2338 / Variant: MG1655 / Plasmid: pETDuet-1 / Cell line (production host): BL21DE3 pLys / Production host: Escherichia coli (E. coli)
References: UniProt: P77399, enoyl-CoA hydratase, 3-hydroxybutyryl-CoA epimerase, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris, 1.8 M ammonium sulfate, 4.5 % glycerol, pH 8.0, and 5 % 1,4-dioxane
Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 2.82→107.67 Å / Num. obs: 28799 / % possible obs: 84.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 62.5 Å2 / CC1/2: 1 / Rpim(I) all: 0.094 / Net I/σ(I): 4.8
Reflection shellResolution: 2.82→3.15 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1440 / CC1/2: 0.6 / Rpim(I) all: 0.515 / % possible all: 61.5

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Processing

Software
NameVersionClassification
autoPROCdata collection
STARANISOdata scaling
Aimlessdata scaling
PHASERphasing
PHENIX1.16_3549refinement
Cootmodel building
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YSV

6ysv


Resolution: 2.82→85.72 Å / SU ML: 0.3369 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.5865
RfactorNum. reflection% reflection
Rfree0.2544 1417 4.95 %
Rwork0.2 --
obs0.2027 28628 59.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.2 Å2
Refinement stepCycle: LAST / Resolution: 2.82→85.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10435 0 113 19 10567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310712
X-RAY DIFFRACTIONf_angle_d0.572514540
X-RAY DIFFRACTIONf_chiral_restr0.0421677
X-RAY DIFFRACTIONf_plane_restr0.00441899
X-RAY DIFFRACTIONf_dihedral_angle_d19.18366450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.920.375190.3414131X-RAY DIFFRACTION2.95
2.92-3.030.3301120.3555457X-RAY DIFFRACTION9.79
3.03-3.170.3478600.29371025X-RAY DIFFRACTION22.88
3.17-3.340.3136990.28512153X-RAY DIFFRACTION47.17
3.34-3.550.26621080.2712067X-RAY DIFFRACTION45.53
3.55-3.820.32181840.23313302X-RAY DIFFRACTION72.88
3.82-4.210.29272380.21044355X-RAY DIFFRACTION95.73
4.21-4.810.21492180.1644567X-RAY DIFFRACTION99.27
4.81-6.070.24262390.1994558X-RAY DIFFRACTION99.09
6.07-85.720.22282500.17264596X-RAY DIFFRACTION98.54
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)
13.09010946688-0.252245877498-1.4969367042.517303474790.2258440533216.16178833717-0.08914660623080.420930698904-0.211658824734-0.275275378980.23497772907-0.457986458318-0.3304079958430.759067752322-0.1220933730120.40750470578-0.104123157671-0.08611704550920.474149235365-0.08632498623940.557135470928-34.264241130443.20028746811.9453061024
21.929104979580.9978716673550.4340724617871.598235400510.8603699283142.309002498540.1312246245590.02921687464070.1774917673510.181870810881-0.0712442705729-0.547685046693-0.2537185938550.65813156605-0.06827659488910.4324529492060.00301617079092-0.145842006650.331895414191-0.0029405485770.613394817565-41.268101877342.650115316425.6346835758
33.0555933196-0.504650985480.5032201036691.3586743729-0.3314392959592.354180853270.113079911577-0.00929644983120.2875506476690.278059035108-0.02420062867-0.194133039396-0.06386452525590.0196278634101-0.07840932849280.296355879808-0.0802678629093-0.03268641658470.03638305685080.03019453718490.371383114693-71.075663009937.002019521928.3154893587
42.940732343510.9717939130462.467374296141.51337189759-0.09829325457554.832690477350.1587458229750.1269485262620.365101684748-0.276094899525-0.1894793364950.25771666995-0.125670393885-0.4149905905990.009205891013030.3349260994470.02695314922620.03166572336110.293134831565-0.08775355452130.261510391647-48.8117903745-3.7509943398624.7254706317
51.40762084807-0.4334515022130.7423293726180.417170405956-0.4531391383921.487346833690.6198355891060.0315385348652-0.930471847843-0.330294142726-0.3887786183980.3007727835040.655225443687-0.218966601333-0.07678452710940.554846835937-0.126436589198-0.0699203600930.348320750842-0.2506941111950.167250266831-39.9430010654-11.894416757630.7378217884
62.28316343737-0.575955925615-1.466498721630.5504204883310.2168424652593.99718073663-0.04847224189350.0929261210452-0.2136636536210.05180149777120.07456949511650.03004923456740.279817218063-0.0227573266938-0.08651049634450.185812352183-0.0753332271354-0.02269424663280.163324671166-0.07911596687210.186459281608-8.03020615873-4.8335481179632.933447708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 193 )
2X-RAY DIFFRACTION2chain 'B' and (resid 194 through 309 )
3X-RAY DIFFRACTION3chain 'B' and (resid 310 through 710 )
4X-RAY DIFFRACTION4chain 'A' and (resid 4 through 170 )
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 309 )
6X-RAY DIFFRACTION6chain 'A' and (resid 310 through 710 )

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