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

ID or keywords:

Entry

Database: PDB / ID: 6hxq

Title

Structure of citryl-CoA synthetase from Hydrogenobacter thermophilus

Components

Citryl-CoA synthetase large subunit
Citryl-CoA synthetase small subunit

Keywords

LYASE / 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 / ATP citrate synthase / ligase activity / catalytic activity / tricarboxylic acid cycle / ATP binding
Similarity search - Function

Biological species

Hydrogenobacter thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.91 Å

Authors

Verstraete, K. / Verschueren, K.

Funding support

Belgium, 1items

Citation

Journal: 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

Deposition	Oct 17, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 10, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	May 8, 2019	Group: 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 1.3	Jan 24, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6hxq.cif.gz	603.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6hxq.ent.gz	507.1 KB	Display	PDB format
PDBx/mmJSON format	6hxq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hx/6hxq ftp://data.pdbj.org/pub/pdb/validation_reports/hx/6hxq	HTTPS FTP

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Related structure data

Related structure data	6hxhC 6hxiC 6hxjC 6hxkC 6hxlC 6hxmC 6hxnC 6hxoC 6hxpC 6qclC 6qfbC 2yv2S 3ufxS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4a09-d 2wh0-d 5bv5-d 5if0-d 6bys-1 4hw6-d 6no7-1 1h0m-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (13) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (2) #192 - Dec 2015 Vancomycin similarity (1) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#154 - Oct 2012
Citric Acid Cycle
similarity (13)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (2)
#192 - Dec 2015
Vancomycin
similarity (1)
#187 - Jul 2015
New Delhi Metallo-β-Lactamase
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#93 - Sep 2007
Citrate Synthase
similarity (1)
#216 - Dec 2017
Biodegradable Plastic
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

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

174 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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.

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 number	19
Space group name H-M	P2₁2₁2₁

#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

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.29 Å³/Da / Density % sol: 62.63 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 25, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00003 Å / Relative weight: 1
Reflection	Resolution: 2.91→47.93 Å / Num. obs: 48328 / % possible obs: 99.5 % / Redundancy: 6.5 % / B_iso Wilson estimate: 84.77 Å² / CC_1/2: 0.998 / R_rim(I) all: 0.153 / Net I/σ(I): 12.83
Reflection shell	Resolution: 2.91→3.08 Å / Mean I/σ(I) obs: 0.83 / Num. unique obs: 7549 / CC_1/2: 0.48 / R_rim(I) all: 2.17 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
BUSTER	2.10.2	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2yv2, 3ufx

2yv2

3ufx

Resolution: 2.91→47.6 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.911 / R_factor R_free error: 0 / SU R Cruickshank DPI: 1.964 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.181 / SU R_free Blow DPI: 0.31 / SU R_free Cruickshank DPI: 0.319

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.223	2409	5 %	RANDOM
R_work	0.189	-	-	-
obs	0.191	48218	99.9 %	-

Displacement parameters

B_iso mean: 99.16 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	21.1312 Å²	0 Å²	0 Å²
2-	-	1.4913 Å²	0 Å²
3-	-	-	-22.6225 Å²

Refine analyze

Luzzati coordinate error obs: 0.4 Å

Refinement step

Cycle: 1 / Resolution: 2.91→47.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11552	0	149	0	11701

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	12059	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.21	16468	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		4180	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		268	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1762	HARMONIC	5
X-RAY DIFFRACTION	t_it		12059	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.88
X-RAY DIFFRACTION	t_other_torsion	19.51
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		1564	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		13863	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.91→2.99 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.265	175	5.03 %
R_work	0.24	3304	-
all	0.241	3479	-
obs	-	-	99.52 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.7439	1.9908	0.0279	5.2506	2.813	6.4144	-0.0068	0.3811	0.3202	-0.5442	0.0362	-0.5007	0.5438	-0.0405	-0.0294	0.1908	-0.0044	0.0779	0.1996	0.152	-0.304	-17.7825	-45.3702	17.4532
2	0.1973	-1.5546	-2.077	1.0156	1.9761	0.4315	-0.0305	0.1837	-0.1649	-0.2387	0.0018	-0.1776	0.0506	0.1426	0.0287	0.1863	-0.0256	0.152	0.2865	0.0847	-0.304	-18.1162	-55.1477	18.9461
3	5.9556	2.9104	-2.9104	4.0556	1.08	0.6056	-0.0949	0.063	0.2144	0.1417	-0.084	0.0749	0.2656	0.0241	0.1789	0.0364	-0.088	-0.0189	0.1549	0.0306	-0.2475	-24.3348	-50.5191	32.6132
4	1.9757	0.0204	-0.2126	5.4493	-0.9328	3.751	0.0987	-0.0654	0.4707	0.3343	-0.4012	-0.5258	-0.4983	-0.2012	0.3025	-0.1783	-0.0868	0.0159	-0.0215	0.0522	0.0281	-18.0396	-30.8802	32.1234
5	1.0835	2.873	-2.0952	6.3049	1.625	5.9081	-0.0025	-0.038	-0.0259	0.0884	0.0232	0.0168	-0.3738	-0.1871	-0.0207	-0.084	-0.1421	0.0107	-0.0508	0.0252	-0.0085	-26.6311	-27.3657	41.786
6	3.107	1.4903	-1.5053	3.8103	-0.3708	4.0703	-0.0089	-0.1988	0.5293	0.5442	-0.1892	-0.3113	-0.3503	-0.236	0.1982	0.1889	-0.152	-0.024	-0.1701	-0.1043	-0.1869	-22.0393	-22.1973	40.4317
7	0	1.0395	-0.3927	3.1754	1.3673	0.0001	0.0237	-0.0866	0.0314	0.0538	-0.0671	0.0293	-0.1532	-0.0247	0.0433	0.2742	0.1407	-0.0224	-0.2857	-0.0187	0.1982	-33.4118	-2.2193	19.2844
8	0.1055	0.1419	0.6639	0.5317	-0.6151	0.274	-0.0094	0.0278	0.0183	-0.0085	-0.0727	0.0384	-0.0303	-0.1291	0.0821	-0.0727	-0.14	0.1117	0.1213	-0.0027	-0.0223	-23.8932	-39.2844	26.6661
9	4.3286	-0.4555	-0.1446	2.3659	-0.2288	3.5041	-0.0485	-0.2469	0.5432	0.5442	0.2346	0.5442	-0.5442	-0.5442	-0.1862	0.072	0.1009	0.152	-0.235	0.0691	-0.2023	-46.2459	-50.5128	57.5572
10	0.0037	-1.5959	1.1418	0.5001	-1.3489	1.1965	0.0093	-0.0707	0.0929	-0.0119	-0.0377	0.0614	-0.0607	-0.0981	0.0284	-0.2023	-0.0751	0.0131	0.2799	0.0358	0.0808	-50.3276	-43.3385	36.1509
11	6.6599	-1.2435	0.6281	2.9491	0.7531	2.2953	-0.1008	-0.4467	0.4844	-0.1155	-0.2204	0.5442	-0.5078	-0.5442	0.3212	-0.2551	0.152	-0.0603	-0.0537	-0.152	-0.0052	-43.1824	-18.1667	20.0958
12	0	-0.085	-0.0499	0.0668	-0.0201	0	0.0021	-0.0063	-0.0012	0.0022	-0.0083	-0.0036	0.0078	-0.0028	0.0062	0.0442	0.0625	0.1225	-0.0267	-0.0257	-0.0039	-34.1023	-30.5078	19.0027
13	0.6828	-2.9047	0.4954	3.5649	1.5885	3.7075	-0.0548	-0.2082	-0.3239	0.544	-0.0124	-0.5442	-0.5412	0.1279	0.0672	0.304	-0.0708	-0.0619	0.0751	0.152	-0.304	-20.5023	-79.0821	69.0093
14	0	-1.1566	-1.1873	0	2.9037	4.5007	-0.0389	-0.1527	0.0847	0.3503	-0.0074	0.0297	-0.2308	0.1701	0.0462	0.304	-0.152	-0.152	0.004	0.1165	-0.304	-21.7849	-69.3701	67.4898
15	3.1792	-2.747	2.9005	3.7339	-0.3323	0.4865	-0.0537	0.09	-0.1877	0.0928	-0.0808	-0.0311	-0.2142	0.2923	0.1345	0.0965	0.0468	0.0273	0.1324	0.0257	-0.2188	-24.7695	-74.498	52.9223
16	0.7856	-1.6695	-0.2238	4.752	-0.606	2.5141	-0.038	-0.0395	-0.4703	0.0622	-0.3956	-0.3144	0.1967	0.4833	0.4337	-0.206	0.1035	-0.015	0.0398	0.0684	0.0949	-16.2131	-93.1285	54.5598
17	0.023	-2.0359	1.1916	3.4059	-0.0734	4.8579	-0.0163	0.0655	-0.1257	-0.3402	-0.0483	0.0102	0.2188	0.0586	0.0646	-0.0768	0.1015	0.0912	-0.0633	-0.0928	0.0318	-24.2934	-94.7053	37.969
18	0.1443	-2.3639	0.3794	4.0651	-0.3843	1.7787	0.0264	0.2391	-0.5416	-0.4952	-0.125	0.1044	0.5306	0.1287	0.0985	-0.1686	0.152	0.014	-0.1871	0.0077	0.2353	-19.2709	-111.134	52.9906
19	0.4615	-0.9395	-0.0215	0.0401	0.3431	0.1106	-0.0095	-0.0572	-0.0998	0.0259	-0.0351	-0.0198	0.0745	-0.0347	0.0446	-0.0626	0.1436	-0.0813	0.0848	-0.0343	-0.005	-23.4741	-85.7316	58.6568
20	4.7704	2.0017	0.608	3.1865	0.459	3.9882	-0.0894	0.4925	-0.4232	-0.5442	0.4502	0.5442	0.5442	-0.5442	-0.3608	-0.0222	-0.152	-0.1491	-0.0649	0.0254	-0.304	-41.7252	-76.8584	24.582
21	0.4681	-0.225	0.4974	1.807	-0.9893	2.081	0.033	0.1626	-0.5442	-0.3132	0.2732	0.5442	0.5442	-0.5442	-0.3063	-0.304	-0.0908	0.0842	-0.1504	0.0139	0.304	-41.7905	-107.057	59.657

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|4 - A\|59 }
2	X-RAY DIFFRACTION	2	{ A\|60 - A\|83 }
3	X-RAY DIFFRACTION	3	{ A\|84 - A\|134 }
4	X-RAY DIFFRACTION	4	{ A\|135 - A\|241 }
5	X-RAY DIFFRACTION	5	{ A\|242 - A\|267 }
6	X-RAY DIFFRACTION	6	{ A\|268 - A\|323 }
7	X-RAY DIFFRACTION	7	{ A\|324 - A\|345 }
8	X-RAY DIFFRACTION	8	{ A\|401 - A\|402 }
9	X-RAY DIFFRACTION	9	{ B\|1 - B\|214 }
10	X-RAY DIFFRACTION	10	{ B\|215 - B\|237 }
11	X-RAY DIFFRACTION	11	{ B\|238 - B\|410 }
12	X-RAY DIFFRACTION	12	{ B\|501 - B\|501 }
13	X-RAY DIFFRACTION	13	{ C\|4 - C\|59 }
14	X-RAY DIFFRACTION	14	{ C\|60 - C\|83 }
15	X-RAY DIFFRACTION	15	{ C\|84 - C\|134 }
16	X-RAY DIFFRACTION	16	{ C\|135 - C\|241 }
17	X-RAY DIFFRACTION	17	{ C\|242 - C\|279 }
18	X-RAY DIFFRACTION	18	{ C\|280 - C\|345 }
19	X-RAY DIFFRACTION	19	{ C\|401 - C\|402 }
20	X-RAY DIFFRACTION	20	{ D\|1 - D\|214 }
21	X-RAY DIFFRACTION	21	{ D\|215 - D\|410 }

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