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- PDB-6hxq: Structure of citryl-CoA synthetase from Hydrogenobacter thermophilus -

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Basic information

Entry
Database: PDB / ID: 6hxq
TitleStructure of citryl-CoA synthetase from Hydrogenobacter thermophilus
Components
  • Citryl-CoA synthetase large subunit
  • Citryl-CoA synthetase small subunit
KeywordsLYASE / Citryl-CoA synthesise / ATP citrate lyase / central metabolism / acetyl-Coa / citrate shuttle / rTCA cycle / citryl-CoA / lipogenesis
Function / homology
Function and homology information


ATP citrate synthase activity / ligase activity / catalytic activity / tricarboxylic acid cycle / ATP binding
Similarity search - Function
Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain ...Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, subdomain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / CITRATE ANION / TRIETHYLENE GLYCOL / Citryl-CoA synthetase small subunit / Citryl-CoA synthetase large subunit
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsVerstraete, K. / Verschueren, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders1524918N Belgium
CitationJournal: Nature / Year: 2019
Title: Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.
Authors: Verschueren, K.H.G. / Blanchet, C. / Felix, J. / Dansercoer, A. / De Vos, D. / Bloch, Y. / Van Beeumen, J. / Svergun, D. / Gutsche, I. / Savvides, S.N. / Verstraete, K.
History
DepositionOct 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citryl-CoA synthetase small subunit
B: Citryl-CoA synthetase large subunit
C: Citryl-CoA synthetase small subunit
D: Citryl-CoA synthetase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,76311
Polymers171,4384
Non-polymers2,3257
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The proposed biological assembly is based on the structural homology with heterotetrameric succinyl-CoA synthetase.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18840 Å2
ΔGint-40 kcal/mol
Surface area58420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.495, 127.029, 143.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Citryl-CoA synthetase small subunit


Mass: 38085.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria)
Gene: ccsB / Plasmid: pET-DUET / Production host: Escherichia coli (E. coli) / References: UniProt: Q75VW6
#2: Protein Citryl-CoA synthetase large subunit


Mass: 47633.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria)
Gene: ccsA / Plasmid: pET-DUET / Production host: Escherichia coli (E. coli) / References: UniProt: Q75VW8
#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
Has protein modificationY

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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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 18% PEG4000 20% 2-propanol 0.1 M Na-citrate pH 5.6 Protein sample buffer: 20 mM HEPES, 150 mM NaCl, pH 7.4 supplemented with 10 mM CoASH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.91→47.93 Å / Num. obs: 48328 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 84.77 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.153 / Net I/σ(I): 12.83
Reflection shellResolution: 2.91→3.08 Å / Mean I/σ(I) obs: 0.83 / Num. unique obs: 7549 / CC1/2: 0.48 / Rrim(I) all: 2.17 / % possible all: 97.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yv2, 3ufx

2yv2

3ufx


Resolution: 2.91→47.6 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.964 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.181 / SU Rfree Blow DPI: 0.31 / SU Rfree Cruickshank DPI: 0.319
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2409 5 %RANDOM
Rwork0.189 ---
obs0.191 48218 99.9 %-
Displacement parametersBiso mean: 99.16 Å2
Baniso -1Baniso -2Baniso -3
1-21.1312 Å20 Å20 Å2
2--1.4913 Å20 Å2
3----22.6225 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.91→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11552 0 149 0 11701
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112059HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2116468HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4180SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes268HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1762HARMONIC5
X-RAY DIFFRACTIONt_it12059HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion19.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1564SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13863SEMIHARMONIC4
LS refinement shellResolution: 2.91→2.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 175 5.03 %
Rwork0.24 3304 -
all0.241 3479 -
obs--99.52 %
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)
10.74391.99080.02795.25062.8136.4144-0.00680.38110.3202-0.54420.0362-0.50070.5438-0.0405-0.02940.1908-0.00440.07790.19960.152-0.304-17.7825-45.370217.4532
20.1973-1.5546-2.0771.01561.97610.4315-0.03050.1837-0.1649-0.23870.0018-0.17760.05060.14260.02870.1863-0.02560.1520.28650.0847-0.304-18.1162-55.147718.9461
35.95562.9104-2.91044.05561.080.6056-0.09490.0630.21440.1417-0.0840.07490.26560.02410.17890.0364-0.088-0.01890.15490.0306-0.2475-24.3348-50.519132.6132
41.97570.0204-0.21265.4493-0.93283.7510.0987-0.06540.47070.3343-0.4012-0.5258-0.4983-0.20120.3025-0.1783-0.08680.0159-0.02150.05220.0281-18.0396-30.880232.1234
51.08352.873-2.09526.30491.6255.9081-0.0025-0.038-0.02590.08840.02320.0168-0.3738-0.1871-0.0207-0.084-0.14210.0107-0.05080.0252-0.0085-26.6311-27.365741.786
63.1071.4903-1.50533.8103-0.37084.0703-0.0089-0.19880.52930.5442-0.1892-0.3113-0.3503-0.2360.19820.1889-0.152-0.024-0.1701-0.1043-0.1869-22.0393-22.197340.4317
701.0395-0.39273.17541.36730.00010.0237-0.08660.03140.0538-0.06710.0293-0.1532-0.02470.04330.27420.1407-0.0224-0.2857-0.01870.1982-33.4118-2.219319.2844
80.10550.14190.66390.5317-0.61510.274-0.00940.02780.0183-0.0085-0.07270.0384-0.0303-0.12910.0821-0.0727-0.140.11170.1213-0.0027-0.0223-23.8932-39.284426.6661
94.3286-0.4555-0.14462.3659-0.22883.5041-0.0485-0.24690.54320.54420.23460.5442-0.5442-0.5442-0.18620.0720.10090.152-0.2350.0691-0.2023-46.2459-50.512857.5572
100.0037-1.59591.14180.5001-1.34891.19650.0093-0.07070.0929-0.0119-0.03770.0614-0.0607-0.09810.0284-0.2023-0.07510.01310.27990.03580.0808-50.3276-43.338536.1509
116.6599-1.24350.62812.94910.75312.2953-0.1008-0.44670.4844-0.1155-0.22040.5442-0.5078-0.54420.3212-0.25510.152-0.0603-0.0537-0.152-0.0052-43.1824-18.166720.0958
120-0.085-0.04990.0668-0.020100.0021-0.0063-0.00120.0022-0.0083-0.00360.0078-0.00280.00620.04420.06250.1225-0.0267-0.0257-0.0039-34.1023-30.507819.0027
130.6828-2.90470.49543.56491.58853.7075-0.0548-0.2082-0.32390.544-0.0124-0.5442-0.54120.12790.06720.304-0.0708-0.06190.07510.152-0.304-20.5023-79.082169.0093
140-1.1566-1.187302.90374.5007-0.0389-0.15270.08470.3503-0.00740.0297-0.23080.17010.04620.304-0.152-0.1520.0040.1165-0.304-21.7849-69.370167.4898
153.1792-2.7472.90053.7339-0.33230.4865-0.05370.09-0.18770.0928-0.0808-0.0311-0.21420.29230.13450.09650.04680.02730.13240.0257-0.2188-24.7695-74.49852.9223
160.7856-1.6695-0.22384.752-0.6062.5141-0.038-0.0395-0.47030.0622-0.3956-0.31440.19670.48330.4337-0.2060.1035-0.0150.03980.06840.0949-16.2131-93.128554.5598
170.023-2.03591.19163.4059-0.07344.8579-0.01630.0655-0.1257-0.3402-0.04830.01020.21880.05860.0646-0.07680.10150.0912-0.0633-0.09280.0318-24.2934-94.705337.969
180.1443-2.36390.37944.0651-0.38431.77870.02640.2391-0.5416-0.4952-0.1250.10440.53060.12870.0985-0.16860.1520.014-0.18710.00770.2353-19.2709-111.13452.9906
190.4615-0.9395-0.02150.04010.34310.1106-0.0095-0.0572-0.09980.0259-0.0351-0.01980.0745-0.03470.0446-0.06260.1436-0.08130.0848-0.0343-0.005-23.4741-85.731658.6568
204.77042.00170.6083.18650.4593.9882-0.08940.4925-0.4232-0.54420.45020.54420.5442-0.5442-0.3608-0.0222-0.152-0.1491-0.06490.0254-0.304-41.7252-76.858424.582
210.4681-0.2250.49741.807-0.98932.0810.0330.1626-0.5442-0.31320.27320.54420.5442-0.5442-0.3063-0.304-0.09080.0842-0.15040.01390.304-41.7905-107.05759.657
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|4 - A|59 }
2X-RAY DIFFRACTION2{ A|60 - A|83 }
3X-RAY DIFFRACTION3{ A|84 - A|134 }
4X-RAY DIFFRACTION4{ A|135 - A|241 }
5X-RAY DIFFRACTION5{ A|242 - A|267 }
6X-RAY DIFFRACTION6{ A|268 - A|323 }
7X-RAY DIFFRACTION7{ A|324 - A|345 }
8X-RAY DIFFRACTION8{ A|401 - A|402 }
9X-RAY DIFFRACTION9{ B|1 - B|214 }
10X-RAY DIFFRACTION10{ B|215 - B|237 }
11X-RAY DIFFRACTION11{ B|238 - B|410 }
12X-RAY DIFFRACTION12{ B|501 - B|501 }
13X-RAY DIFFRACTION13{ C|4 - C|59 }
14X-RAY DIFFRACTION14{ C|60 - C|83 }
15X-RAY DIFFRACTION15{ C|84 - C|134 }
16X-RAY DIFFRACTION16{ C|135 - C|241 }
17X-RAY DIFFRACTION17{ C|242 - C|279 }
18X-RAY DIFFRACTION18{ C|280 - C|345 }
19X-RAY DIFFRACTION19{ C|401 - C|402 }
20X-RAY DIFFRACTION20{ D|1 - D|214 }
21X-RAY DIFFRACTION21{ D|215 - D|410 }

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