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- PDB-5tdm: TEV Cleaved Human ATP Citrate Lyase Bound to 4R-Hydroxycitrate and ADP -

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Basic information

Entry
Database: PDB / ID: 5tdm
TitleTEV Cleaved Human ATP Citrate Lyase Bound to 4R-Hydroxycitrate and ADP
Components(ATP-citrate synthase) x 2
KeywordsTRANSFERASE / TEV cleaved / ATP-grasp fold / 4R hydroxycitrate binding
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 / lipid biosynthetic process / 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 / lipid biosynthetic process / cholesterol biosynthetic process / fatty acid biosynthetic process / azurophil granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / cytosol
Similarity search - Function
ATP-citrate synthase / 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 synthase / 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-L-threo-pentaric acid / ADENOSINE / ADENOSINE-5'-DIPHOSPHATE / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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)84,3949
Polymers83,2582
Non-polymers1,1357
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-43 kcal/mol
Surface area29290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.379, 84.814, 193.869
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, 194 molecules

#3: Chemical ChemComp-7A2 / 3-C-carboxy-2-deoxy-L-threo-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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 13% P3350, 100 mM TrisHCl pH 8.7, 125 mM ammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.00003 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.1→63.77 Å / Num. obs: 53911 / % possible obs: 99.7 % / Redundancy: 5.1 % / Net I/σ(I): 8.3

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Processing

SoftwareName: PHENIX / Version: (1.10_2152: ???) / Classification: refinement
RefinementResolution: 2.1→63.77 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.52
RfactorNum. reflection% reflection
Rfree0.286 2569 4.99 %
Rwork0.216 --
obs0.219 51533 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→63.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5815 0 74 187 6076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136017
X-RAY DIFFRACTIONf_angle_d1.1558154
X-RAY DIFFRACTIONf_dihedral_angle_d14.6993586
X-RAY DIFFRACTIONf_chiral_restr0.063907
X-RAY DIFFRACTIONf_plane_restr0.0081071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0993-2.13970.48251200.39852598X-RAY DIFFRACTION91
2.1397-2.18340.46511440.36772656X-RAY DIFFRACTION95
2.1834-2.23080.4111350.352733X-RAY DIFFRACTION96
2.2308-2.28270.40891460.3292669X-RAY DIFFRACTION95
2.2827-2.33980.34371500.31962678X-RAY DIFFRACTION96
2.3398-2.40310.4181560.30592725X-RAY DIFFRACTION95
2.4031-2.47380.3761400.29682653X-RAY DIFFRACTION95
2.4738-2.55370.34971490.2822709X-RAY DIFFRACTION95
2.5537-2.64490.32751420.27032706X-RAY DIFFRACTION95
2.6449-2.75080.3681350.27442686X-RAY DIFFRACTION95
2.7508-2.8760.32821540.26232665X-RAY DIFFRACTION94
2.876-3.02770.30681550.25742717X-RAY DIFFRACTION95
3.0277-3.21730.33451490.24352671X-RAY DIFFRACTION94
3.2173-3.46570.35191310.21592764X-RAY DIFFRACTION95
3.4657-3.81450.25741350.18952734X-RAY DIFFRACTION95
3.8145-4.36630.23771410.15132791X-RAY DIFFRACTION95
4.3663-5.50060.17821380.14092873X-RAY DIFFRACTION97
5.5006-63.85970.20291490.15752936X-RAY DIFFRACTION95
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)
10.2529-0.0903-0.24280.08310.17170.61830.1916-0.12310.0594-0.0615-0.15840.00330.0309-0.4245-0.04620.3147-0.02470.00820.28710.00020.35691.43423.671320.9638
20.1638-0.1854-0.01350.216-0.03230.12070.22250.0261-0.1337-0.47030.04830.14890.0239-0.00340.15090.3815-0.033-0.07180.1459-0.02230.4894-0.289214.46434.2713
30.2332-0.18770.03180.2218-0.16710.20440.0177-0.08910.1025-0.1929-0.001-0.05880.10950.03010.00610.3385-0.03170.0060.20780.05930.33938.973519.80923.7842
41.3529-0.45570.14350.30460.22340.4125-0.2636-0.43010.33310.00120.1223-0.0956-0.1592-0.1154-0.10540.3883-0.0641-0.05970.3138-0.08720.398713.465235.255726.0716
50.10660.08470.05420.1824-0.13340.217-0.0166-0.20150.0194-0.0457-0.03340.015-0.0694-0.1906-0.0010.3416-0.0399-0.01040.3079-0.00350.33576.459723.856224.5347
60.4628-0.3151-0.22580.6178-0.28820.5134-0.11270.05220.0582-0.41680.22690.1350.4043-0.10160.00020.6739-0.0856-0.07140.58690.09340.405224.9476-11.611225.5553
70.4932-0.20540.21771.1125-0.20220.2842-0.0737-0.4522-0.06860.06040.32650.1729-0.04540.01870.12510.32310.0760.01040.64730.11630.367217.35511.902654.92
80.65820.4173-0.4090.5791-0.35410.27290.0092-0.13440.1791-0.1862-0.04560.00420.07490.2894-00.33740.0182-0.01790.5378-0.01010.372933.41678.698339.4352
90.0209-0.05790.02480.6897-0.30160.12320.014-0.04080.0669-0.2184-0.2388-0.20520.21860.6407-0.01140.35920.09050.01520.77010.13320.446146.66335.541438.6985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:29 )A2 - 29
2X-RAY DIFFRACTION2( CHAIN A AND RESID 30:42 )A30 - 42
3X-RAY DIFFRACTION3( CHAIN A AND RESID 43:108 )A43 - 108
4X-RAY DIFFRACTION4( CHAIN A AND RESID 109:176 )A109 - 176
5X-RAY DIFFRACTION5( CHAIN A AND RESID 177:243 )A177 - 243
6X-RAY DIFFRACTION6( CHAIN A AND RESID 244:431 ) OR ( CHAIN B AND RESID 488:489 )A244 - 431
7X-RAY DIFFRACTION6( CHAIN A AND RESID 244:431 ) OR ( CHAIN B AND RESID 488:489 )B488 - 489
8X-RAY DIFFRACTION7( CHAIN B AND RESID 490:650 )B490 - 650
9X-RAY DIFFRACTION8( CHAIN B AND RESID 651:776 )B651 - 776
10X-RAY DIFFRACTION9( CHAIN B AND RESID 777:810 )B777 - 810

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