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- PDB-5tde: TEV Cleaved Human ATP Citrate Lyase Bound to Citrate -

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Basic information

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


ATP citrate synthase / ATP citrate synthase activity / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process ...ATP citrate synthase / ATP citrate synthase activity / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process / tricarboxylic acid cycle / 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
Succinyl-CoA synthetase domains / ATP-citrate synthase / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / 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. ...Succinyl-CoA synthetase domains / ATP-citrate synthase / ATP-citrate synthase, citrate-binding domain / ATP citrate lyase citrate-binding / 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
DIHYDROGENPHOSPHATE ION / CITRATE ANION / ATP-citrate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsHu, J. / Fraser, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
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 / Refinement description / Category: citation / software
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 / _software.classification
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,07412
Polymers83,1792
Non-polymers89410
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-61 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.828, 84.084, 194.781
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: 35342.598 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 , 5 types, 747 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION / Dihydrogen phosphate


Mass: 96.987 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O4P
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5% P3350, 100 mM Tris-HCL pH 7.0, 125 mM ammonium phosphate pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→51.39 Å / Num. obs: 100886 / % possible obs: 99.4 % / Redundancy: 3.7 % / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.7→51.39 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1842 5021 4.98 %
Rwork0.1551 --
obs0.1566 100805 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→51.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5779 0 54 737 6570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015991
X-RAY DIFFRACTIONf_angle_d0.9688102
X-RAY DIFFRACTIONf_dihedral_angle_d15.1233590
X-RAY DIFFRACTIONf_chiral_restr0.058896
X-RAY DIFFRACTIONf_plane_restr0.0061035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.29061400.26983161X-RAY DIFFRACTION99
1.7193-1.73950.30421660.25153180X-RAY DIFFRACTION99
1.7395-1.76080.27191440.23533119X-RAY DIFFRACTION99
1.7608-1.78310.24731670.22843162X-RAY DIFFRACTION99
1.7831-1.80650.26761770.21793141X-RAY DIFFRACTION99
1.8065-1.83130.24531700.2053136X-RAY DIFFRACTION99
1.8313-1.85740.22411620.20553151X-RAY DIFFRACTION99
1.8574-1.88520.24591690.23132X-RAY DIFFRACTION99
1.8852-1.91460.23661600.18873195X-RAY DIFFRACTION99
1.9146-1.9460.20911770.17813135X-RAY DIFFRACTION99
1.946-1.97960.21611700.17213130X-RAY DIFFRACTION99
1.9796-2.01560.22111690.16843164X-RAY DIFFRACTION99
2.0156-2.05430.19651700.16483172X-RAY DIFFRACTION99
2.0543-2.09630.22081680.15743155X-RAY DIFFRACTION99
2.0963-2.14180.1681560.1533204X-RAY DIFFRACTION99
2.1418-2.19170.16751640.14613166X-RAY DIFFRACTION99
2.1917-2.24650.19861730.13963191X-RAY DIFFRACTION99
2.2465-2.30720.1831480.13943200X-RAY DIFFRACTION99
2.3072-2.37510.16841950.13873175X-RAY DIFFRACTION100
2.3751-2.45180.1731800.13363210X-RAY DIFFRACTION100
2.4518-2.53940.17921760.13673222X-RAY DIFFRACTION100
2.5394-2.64110.151760.13433199X-RAY DIFFRACTION100
2.6411-2.76130.16371510.14183211X-RAY DIFFRACTION100
2.7613-2.90680.17641910.14343243X-RAY DIFFRACTION100
2.9068-3.08890.1671710.13913244X-RAY DIFFRACTION100
3.0889-3.32740.17371800.13933232X-RAY DIFFRACTION100
3.3274-3.66210.17441550.13813258X-RAY DIFFRACTION99
3.6621-4.19190.14091750.13133249X-RAY DIFFRACTION99
4.1919-5.28050.1471460.13773290X-RAY DIFFRACTION98
5.2805-51.4130.2091750.18833357X-RAY DIFFRACTION96

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