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- PDB-5tdf: TEV Cleaved Human ATP Citrate Lyase Bound to 4S hydroxycitrate -

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Basic information

Entry
Database: PDB / ID: 5tdf
TitleTEV Cleaved Human ATP Citrate Lyase Bound to 4S hydroxycitrate
Components(ATP-citrate synthase) x 2
KeywordsTRANSFERASE / TEV cleaved / ATP-grasp fold / 4S Hydroxycitrate
Function / homology
Function and homology information


ATP citrate synthase / ATP citrate synthase activity / citrate metabolic process / Fatty acyl-CoA biosynthesis / acetyl-CoA biosynthetic process / ChREBP activates metabolic gene expression / coenzyme A metabolic process / oxaloacetate metabolic process / negative regulation of ferroptosis / cholesterol biosynthetic process ...ATP citrate synthase / ATP citrate synthase activity / citrate metabolic process / Fatty acyl-CoA biosynthesis / acetyl-CoA biosynthetic process / ChREBP activates metabolic gene expression / coenzyme A metabolic process / oxaloacetate metabolic process / negative regulation of ferroptosis / cholesterol biosynthetic process / lipid biosynthetic process / fatty acid biosynthetic process / azurophil granule lumen / ficolin-1-rich granule lumen / ciliary basal body / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / membrane / cytosol
Similarity search - Function
ATP-citrate synthase / : / 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, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. ...ATP-citrate synthase / : / 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, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-C-carboxy-2-deoxy-D-erythro-pentaric acid / ADENINE / ADENOSINE-5'-DIPHOSPHATE / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsHu, J. / Fraser, M.E.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Binding of hydroxycitrate to human ATP-citrate lyase.
Authors: Hu, J. / Komakula, A. / Fraser, M.E.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-citrate synthase
B: ATP-citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,63013
Polymers83,2582
Non-polymers1,37211
Water14,790821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-43 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.050, 83.870, 195.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ATP-citrate synthase / ATP-citrate (pro-S-)-lyase / ACL / Citrate cleavage enzyme


Mass: 47836.633 Da / Num. of mol.: 1 / Fragment: unp residues 1-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Production host: Escherichia coli (E. coli) / References: UniProt: P53396, ATP citrate synthase
#2: Protein ATP-citrate synthase / ATP-citrate (pro-S-)-lyase / ACL / Citrate cleavage enzyme


Mass: 35421.570 Da / Num. of mol.: 1 / Fragment: unp residues 488-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Production host: Escherichia coli (E. coli) / References: UniProt: P53396, ATP citrate synthase

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Non-polymers , 6 types, 832 molecules

#3: Chemical ChemComp-7A3 / 3-C-carboxy-2-deoxy-D-erythro-pentaric acid


Mass: 208.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O8
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 821 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE AMINO-TERMINAL PORTION OF HUMAN ACLY WAS REDESIGNED TO HAVE TEV PROTEASE CLEAVAGE SITES ...THE AMINO-TERMINAL PORTION OF HUMAN ACLY WAS REDESIGNED TO HAVE TEV PROTEASE CLEAVAGE SITES BORDERING THE LINKER REGION. BOTH CLEAVAGE SITES HAD THE SAME SEQUENCE, ENLYFQS, AND THESE RESIDUES WERE SUBSTITUTED FOR RESIDUES 426-432 AND 481-487 OF ACLY. A HIS10-TAG REPLACED RESIDUES 450-459 OF THE LINKER. THE PROTEIN WAS TERMINATED AT RESIDUE 810. WHEN CLEAVED, THE PROTEIN WOULD CONSIST OF RESIDUES 2-425-ENLYFQ AND S-488-810 OF HACLY.

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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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 15% P3350, 100 mM TrisHCl pH 8.4, 150 mM ammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→41.94 Å / Num. obs: 84385 / % possible obs: 99.6 % / Redundancy: 3.5 % / Net I/σ(I): 8.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
Aimlessdata scaling
RefinementResolution: 1.8→41.94 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.15
RfactorNum. reflection% reflection
Rfree0.191 4236 5.02 %
Rwork0.15 --
obs0.152 84319 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5781 0 89 821 6691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016022
X-RAY DIFFRACTIONf_angle_d0.9948151
X-RAY DIFFRACTIONf_dihedral_angle_d14.4443604
X-RAY DIFFRACTIONf_chiral_restr0.06903
X-RAY DIFFRACTIONf_plane_restr0.0061054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.27641380.2322686X-RAY DIFFRACTION100
1.8205-1.84190.28021440.22752632X-RAY DIFFRACTION100
1.8419-1.86440.28211500.20992635X-RAY DIFFRACTION100
1.8644-1.8880.25461290.20762658X-RAY DIFFRACTION100
1.888-1.91280.22611470.20012652X-RAY DIFFRACTION100
1.9128-1.9390.23321440.19172641X-RAY DIFFRACTION100
1.939-1.96670.23541420.18622697X-RAY DIFFRACTION100
1.9667-1.99610.24121470.17012629X-RAY DIFFRACTION100
1.9961-2.02730.21341360.17492650X-RAY DIFFRACTION100
2.0273-2.06050.2031420.16322667X-RAY DIFFRACTION100
2.0605-2.0960.20371480.16072668X-RAY DIFFRACTION100
2.096-2.13410.2061250.15712674X-RAY DIFFRACTION100
2.1341-2.17520.16971430.15012645X-RAY DIFFRACTION100
2.1752-2.21960.18691230.1432694X-RAY DIFFRACTION100
2.2196-2.26780.18141480.14332680X-RAY DIFFRACTION100
2.2678-2.32060.20591340.13682657X-RAY DIFFRACTION100
2.3206-2.37860.17421660.14042654X-RAY DIFFRACTION100
2.3786-2.44290.18811430.1362665X-RAY DIFFRACTION100
2.4429-2.51480.19871470.13532694X-RAY DIFFRACTION100
2.5148-2.5960.18181450.13922652X-RAY DIFFRACTION100
2.596-2.68870.16281430.14012688X-RAY DIFFRACTION100
2.6887-2.79630.20841280.1422706X-RAY DIFFRACTION100
2.7963-2.92360.18961580.14532681X-RAY DIFFRACTION100
2.9236-3.07770.17481490.14472679X-RAY DIFFRACTION99
3.0777-3.27040.21691510.14012669X-RAY DIFFRACTION99
3.2704-3.52280.18531250.14032706X-RAY DIFFRACTION99
3.5228-3.87710.16771350.1332691X-RAY DIFFRACTION98
3.8771-4.43760.15651320.12162686X-RAY DIFFRACTION97
4.4376-5.58880.14071340.13282675X-RAY DIFFRACTION95
5.5888-41.94640.19851400.17542672X-RAY DIFFRACTION91

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