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- PDB-6hxi: Structure of ATP citrate lyase from Methanothrix soehngenii in co... -

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Basic information

Entry
Database: PDB / ID: 6hxi
TitleStructure of ATP citrate lyase from Methanothrix soehngenii in complex with citrate and coenzyme A
Components
  • Citrate lyase, subunit 1
  • Succinyl-CoA ligase (ADP-forming) subunit alpha
KeywordsLYASE / ATP citrate lyase / central metabolism / acetyl-Coa / citrate shuttle / rTCA cycle / citryl-CoA / lipogenesis
Function / homology
Function and homology information


acetate-CoA ligase (ADP-forming) activity / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / ATP citrate synthase / ATP citrate synthase activity / succinyl-CoA metabolic process / acetyl-CoA biosynthetic process / tricarboxylic acid cycle / lipid metabolic process ...acetate-CoA ligase (ADP-forming) activity / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / ATP citrate synthase / ATP citrate synthase activity / succinyl-CoA metabolic process / acetyl-CoA biosynthetic process / tricarboxylic acid cycle / lipid metabolic process / fatty acid biosynthetic process / lyase activity / ATP binding / cytosol
Similarity search - Function
D-amino Acid Aminotransferase; Chain A, domain 1 - #110 / ATP-grasp domain / : / ATP-citrate synthase 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 ...D-amino Acid Aminotransferase; Chain A, domain 1 - #110 / ATP-grasp domain / : / ATP-citrate synthase 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 / Citrate synthase-like, large alpha subdomain / Succinyl-CoA synthetase-like / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / ATP-grasp fold, A domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / COENZYME A / CITRATE ANION / TRIETHYLENE GLYCOL / SUCCINIC ACID / ATP citrate synthase / Succinyl-CoA ligase (ADP-forming) subunit alpha
Similarity search - Component
Biological speciesMethanosaeta concilii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Nov 13, 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: Citrate lyase, subunit 1
B: Succinyl-CoA ligase (ADP-forming) subunit alpha
C: Citrate lyase, subunit 1
D: Succinyl-CoA ligase (ADP-forming) subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,74917
Polymers233,0004
Non-polymers2,74913
Water13,043724
1
A: Citrate lyase, subunit 1
B: Succinyl-CoA ligase (ADP-forming) subunit alpha
C: Citrate lyase, subunit 1
D: Succinyl-CoA ligase (ADP-forming) subunit alpha
hetero molecules

A: Citrate lyase, subunit 1
B: Succinyl-CoA ligase (ADP-forming) subunit alpha
C: Citrate lyase, subunit 1
D: Succinyl-CoA ligase (ADP-forming) subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)471,49834
Polymers466,0008
Non-polymers5,49826
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area67020 Å2
ΔGint-288 kcal/mol
Surface area147590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.451, 275.020, 72.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Citrate lyase, subunit 1


Mass: 47307.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ACL-A subunit of the heteromeric ACL-A/B ATP citrate lyase
Source: (gene. exp.) Methanosaeta concilii (archaea) / Plasmid: pET11a / Details (production host): Bicistronic construct / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W8FB26, ATP citrate synthase
#2: Protein Succinyl-CoA ligase (ADP-forming) subunit alpha


Mass: 69192.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ACL-B subunit of the heteromeric ACL-A/B ATP citrate lyase
Source: (gene. exp.) Methanosaeta concilii (archaea) / Plasmid: pET11a / Details (production host): Bicistronic construct / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1V4VDZ9, succinate-CoA ligase (ADP-forming)

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Non-polymers , 8 types, 737 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 14% PEG3350 4% tacsimate pH 8.0 Protein sample buffer: 20 mM citrate pH 6.0, 150 mM NaCl 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: 2.1→39.1 Å / Num. obs: 138565 / % possible obs: 99.4 % / Redundancy: 6.1 % / Biso Wilson estimate: 38.49 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.112 / Net I/σ(I): 13.07
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.09 / Num. unique obs: 21584 / CC1/2: 0.387 / Rrim(I) all: 0.1415 / % possible all: 97.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ACL structure from C. limicola

Resolution: 2.1→30.75 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.208 6962 5.03 %RANDOM
Rwork0.179 ---
obs0.181 138531 99.4 %-
Displacement parametersBiso mean: 63.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.9937 Å20 Å20 Å2
2---4.4494 Å20 Å2
3---3.4557 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.1→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15704 0 177 724 16605
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116320HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0722068HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5762SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes387HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2398HARMONIC5
X-RAY DIFFRACTIONt_it16320HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion18.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2123SEMIHARMONIC5
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_contact19158SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 505 5.24 %
Rwork0.228 9138 -
all0.229 9643 -
obs--94.25 %
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)
12.6175-0.9027-1.91241.87840.50471.4108-0.0398-0.21260.18410.29110.32860.3944-0.2326-0.1859-0.2888-0.3040.07170.11840.17150.05280.1166-6.7054-16.019738.3187
20.9261-0.5293-0.16991.79972.78432.04850.0324-0.06820.05570.105-0.00110.049-0.0796-0.0691-0.03130.0130.01260.14650.108-0.0419-0.1392-1.632-20.525161.3791
31.401-0.0668-1.09320-1.63640.13120.0092-0.0656-0.01640.0033-0.0142-0.0016-0.0216-0.02050.0049-0.0587-0.05550.06970.1062-0.01650.016710.3928-20.920448.6092
41.73390.43250.31331.1411-0.2741.7227-0.0295-0.5442-0.5420.17260.0002-0.15710.39890.21680.0294-0.1107-0.03450.0571-0.06580.1520.032928.0634-40.573740.1333
54.7694-1.1213-1.28231.5771-0.15923.1857-0.05150.37220.0279-0.0807-0.0967-0.32490.2870.48390.1482-0.17350.10540.1194-0.07590.04320.0296106.263-48.6304-7.4469
62.08860.1019-1.44631.5340.01264.7628-0.01050.23730.0123-0.3007-0.1119-0.11740.12290.03810.1225-0.20160.14810.1520.30280.1078-0.304100.091-47.7564-30.3132
71.2124-1.30520.10430.4442-0.14070.87430.00330.1536-0.0311-0.0242-0.04330.0148-0.0216-0.01490.040.04720.03250.09720.03230.0303-0.001189.1564-44.0844-16.744
82.14390.0769-0.37841.2071-0.20041.4686-0.05710.5252-0.3288-0.3879-0.02280.20150.1504-0.32230.07990.0256-0.0544-0.0033-0.1386-0.1195-0.064464.2387-51.1289-8.3714
91.8831-0.1999-0.32991.54090.21911.0091-0.1498-0.1116-0.50640.140.1005-0.06950.33970.19340.0493-0.01640.07530.0554-0.24860.04050.030278.4099-53.430214.1121
100.2083-1.1949-0.29663.2253-0.29460-0.0169-0.1604-0.2571-0.001-0.12850.12470.14030.08060.14550.0703-0.04980.0783-0.17520.09320.129454.834-47.841219.2144
110.35950.0112-0.00460.519-0.02670.2671-0.00840.03650.0491-0.1226-0.01060.1006-0.0686-0.03080.0190.1025-0.0448-0.0113-0.0792-0.0107-0.113251.55965.21541.957
124.46070.8331-1.42291.1821-0.22411.9587-0.30080.1788-0.5442-0.22960.09120.16070.3964-0.43630.2096-0.2029-0.152-0.0088-0.1741-0.039-0.036714.4759-34.884317.7531
132.29940.25820.83301.09670.0008-0.04620.0011-0.25940.0628-0.16590.17760.14860.01460.21210.0879-0.12120.081-0.15580.00860.099837.2234-42.653112.4299
140.2750.0583-0.00470.66730.0650.4828-0.0093-0.06460.01590.004-0.0151-0.1547-0.00520.08420.02450.0353-0.04520.0088-0.05020.0142-0.103369.09750.744629.8188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|25 A|115 - A|228 }
2X-RAY DIFFRACTION2{ A|26 - A|114 }
3X-RAY DIFFRACTION3{ A|229 - A|244 }
4X-RAY DIFFRACTION4{ A|245 - A|1111 }
5X-RAY DIFFRACTION5{ C|1 - C|25 C|115 - C|228 }
6X-RAY DIFFRACTION6{ C|26 - C|114 }
7X-RAY DIFFRACTION7{ C|229 - C|244 }
8X-RAY DIFFRACTION8{ C|245 - C|1111 }
9X-RAY DIFFRACTION9{ B|1 - B|323 }
10X-RAY DIFFRACTION10{ B|324 - B|353 }
11X-RAY DIFFRACTION11{ B|354 - B|1000 }
12X-RAY DIFFRACTION12{ D|1 - D|323 }
13X-RAY DIFFRACTION13{ D|324 - D|353 }
14X-RAY DIFFRACTION14{ D|354 - D|1000 }

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