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- PDB-6eqo: Tri-functional propionyl-CoA synthase of Erythrobacter sp. NAP1 w... -

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Basic information

Entry
Database: PDB / ID: 6eqo
TitleTri-functional propionyl-CoA synthase of Erythrobacter sp. NAP1 with bound NADP+ and phosphomethylphosphonic acid adenylate ester
ComponentsAcetyl-coenzyme A synthetase
KeywordsOXIDOREDUCTASE / 3-hydroxpropionyl-CoA synthetase / 3-hydroxpropionyl-CoA dehydratase / acrylyl-CoA reductase / central carbon metabolism / carbon dioxode fixation / 3-hydroxypropionate bi-cycle / natural fusion enzyme / substrate channeling
Function / homology
Function and homology information


3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase activity
Similarity search - Function
Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / AMP-binding, conserved site ...Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GroES-like superfamily / ClpP/crotonase-like domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-hydroxyacyl-CoA dehydrogenase
Similarity search - Component
Biological speciesErythrobacter sp. NAP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsZarzycki, J. / Bernhardsgruetter, I. / Voegeli, B. / Wagner, T. / Engilberge, S. / Girard, E. / Shima, S. / Erb, T.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite.
Authors: Bernhardsgrutter, I. / Vogeli, B. / Wagner, T. / Peter, D.M. / Cortina, N.S. / Kahnt, J. / Bange, G. / Engilberge, S. / Girard, E. / Riobe, F. / Maury, O. / Shima, S. / Zarzycki, J. / Erb, T.J.
History
DepositionOct 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-coenzyme A synthetase
B: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,7526
Polymers401,2552
Non-polymers2,4974
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-50 kcal/mol
Surface area125560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)383.414, 86.740, 133.958
Angle α, β, γ (deg.)90.000, 108.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Acetyl-coenzyme A synthetase / tri-functional propionyl-CoA synthase


Mass: 200627.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: natural fusion enzyme with three catalytic domains / Source: (gene. exp.) Erythrobacter sp. NAP1 (bacteria) / Gene: NAP1_02725 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3WE14
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.63 Å3/Da / Density % sol: 53.16 % / Description: thin needles
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 1 part protein solution (10 mg/mL protein in 20 mM Tris-HCl, pH 7.9, 150 mM sodium chloride, 2 mM CoA, 2 mM NADP+, 2 mM beta,gamma-methylene-ATP) + 1 part buffer (0.1 M BisTris, pH 6.5, 0.2 ...Details: 1 part protein solution (10 mg/mL protein in 20 mM Tris-HCl, pH 7.9, 150 mM sodium chloride, 2 mM CoA, 2 mM NADP+, 2 mM beta,gamma-methylene-ATP) + 1 part buffer (0.1 M BisTris, pH 6.5, 0.2 M sodium acetate, 25% w/v PEG3350, 3% w/v trimethylamine N-oxide dihydrate)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.7→46.18 Å / Num. obs: 112000 / % possible obs: 97.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 46.49 Å2 / CC1/2: 0.958 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.14 / Rrim(I) all: 0.255 / Net I/σ(I): 4.2 / Num. measured all: 349063 / Scaling rejects: 222
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.752.70.8861444152600.1890.6261.0921.794.2
14.79-46.183.40.11425167360.9630.0720.1358.396.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata collection
Aimless0.5.26data scaling
PHENIXphasing
PDB_EXTRACT3.22data extraction
iMOSFLM7data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→46.179 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.48
RfactorNum. reflection% reflection
Rfree0.2289 2007 1.79 %
Rwork0.1907 --
obs0.1914 111918 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.39 Å2 / Biso mean: 52.815 Å2 / Biso min: 19.17 Å2
Refinement stepCycle: final / Resolution: 2.7→46.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27636 0 150 432 28218
Biso mean--51.74 42.07 -
Num. residues----3607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00628434
X-RAY DIFFRACTIONf_angle_d0.76538691
X-RAY DIFFRACTIONf_chiral_restr0.2854212
X-RAY DIFFRACTIONf_plane_restr0.0055121
X-RAY DIFFRACTIONf_dihedral_angle_d21.73510268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.76750.34961360.28667524766095
2.7675-2.84240.3211440.26937903804799
2.8424-2.9260.32391430.25657840798398
2.926-3.02040.28671420.24017887802998
3.0204-3.12830.28571440.23397886803098
3.1283-3.25360.27121410.22057792793398
3.2536-3.40160.23781410.21447667780896
3.4016-3.58090.2531500.19087883803398
3.5809-3.80510.23871440.19067919806398
3.8051-4.09870.19671430.16827902804598
4.0987-4.51090.20871430.15267771791497
4.5109-5.16290.17551480.15048005815399
5.1629-6.50180.20141420.17937832797497
6.5018-46.18590.17811460.16938100824697
Refinement TLS params.Method: refined / Origin x: -56.9361 Å / Origin y: 41.2574 Å / Origin z: 15.9602 Å
111213212223313233
T0.2644 Å20.0453 Å2-0.0552 Å2-0.2211 Å2-0.0477 Å2--0.2681 Å2
L0.4873 °20.1502 °2-0.2009 °2-0.156 °2-0.0385 °2--0.3922 °2
S0.0381 Å °-0.0624 Å °-0.0436 Å °0.0241 Å °-0.0566 Å °0.0316 Å °0.0312 Å °-0.0124 Å °0.0178 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA23 - 1843
2X-RAY DIFFRACTION1allA1900 - 1920
3X-RAY DIFFRACTION1allB23 - 1843
4X-RAY DIFFRACTION1allB1900 - 1920
5X-RAY DIFFRACTION1allS1 - 432

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