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- PDB-7mst: Phosphorylated human E105Qa GTP-specific succinyl-CoA synthetase ... -

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Basic information

Entry
Database: PDB / ID: 7mst
TitlePhosphorylated human E105Qa GTP-specific succinyl-CoA synthetase complexed with coenzyme A
Components(Succinate--CoA ligase ...) x 2
KeywordsLIGASE / Complex
Function / homology
Function and homology information


succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinate metabolic process / succinyl-CoA catabolic process / succinyl-CoA metabolic process ...succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinate metabolic process / succinyl-CoA catabolic process / succinyl-CoA metabolic process / Citric acid cycle (TCA cycle) / tricarboxylic acid cycle / Mitochondrial protein degradation / GDP binding / mitochondrial matrix / nucleotide binding / protein-containing complex binding / GTP binding / magnesium ion binding / mitochondrion / RNA binding / ATP binding / plasma membrane
Similarity search - Function
Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial / Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / 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 ...Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial / Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / 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 / ATP-grasp fold, subdomain 1 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
COENZYME A / Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial / Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsHuang, J. / Fraser, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04815-2019 Canada
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the catalytic mechanism of ATP-citrate lyase
Authors: Huang, J. / Fraser, M.E.
History
DepositionMay 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
B: Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4338
Polymers76,2652
Non-polymers1,1686
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-19 kcal/mol
Surface area28050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.820, 82.927, 48.828
Angle α, β, γ (deg.)90.000, 103.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Succinate--CoA ligase ... , 2 types, 2 molecules AB

#1: Protein Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial / Succinyl-CoA synthetase subunit alpha / SCS-alpha


Mass: 33605.332 Da / Num. of mol.: 1 / Mutation: E105Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P53597, succinate-CoA ligase (GDP-forming), succinate-CoA ligase (ADP-forming)
#2: Protein Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial / GTP-specific succinyl-CoA synthetase subunit beta / G-SCS / GTPSCS / Succinyl-CoA synthetase beta-G ...GTP-specific succinyl-CoA synthetase subunit beta / G-SCS / GTPSCS / Succinyl-CoA synthetase beta-G chain / SCS-betaG


Mass: 42659.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLG2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96I99, succinate-CoA ligase (GDP-forming)

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Non-polymers , 4 types, 451 molecules

#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: Polyethylene glycol 3350, sodium fluoride, Tris-HCl pH 7.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→59.5 Å / Num. obs: 87400 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.03 Å2 / Rpim(I) all: 0.064 / Rrim(I) all: 0.12 / Net I/σ(I): 6.3 / Num. measured all: 302968
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.61-1.643.60.41537143070.7971.52497.9
4.37-59.543.729.51680245150.0280.055100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WCV

6wcv


Resolution: 1.61→46.34 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 5869 6.72 %
Rwork0.1784 81423 -
obs0.1797 87292 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.58 Å2 / Biso mean: 30.739 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 1.61→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5259 0 143 445 5847
Biso mean--31.6 33.15 -
Num. residues----701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.61-1.630.34341490.33392704285396
1.63-1.650.3361160.3222704282099
1.65-1.670.33051380.31572770290898
1.67-1.690.33061260.30162745287198
1.69-1.710.31841280.29082735286399
1.71-1.730.28831300.27672746287699
1.73-1.760.30921700.26482723289398
1.76-1.790.29211470.24982731287899
1.79-1.810.28471280.24822780290899
1.81-1.840.25331330.24792750288399
1.84-1.870.28481220.2372752287499
1.87-1.910.26311450.23062762290799
1.91-1.950.26371430.24262783292699
1.95-1.990.23141330.21512732286599
1.99-2.030.22381330.19332801293499
2.03-2.080.20921450.18622747289299
2.08-2.130.1941300.17412787291799
2.13-2.190.22011590.175627872946100
2.19-2.250.1981910.17782698288999
2.25-2.320.18412940.171326322926100
2.32-2.40.19992670.165626592926100
2.41-2.50.20733040.171326252929100
2.5-2.620.21623060.163226122918100
2.62-2.750.18862830.165526662949100
2.75-2.930.19072970.165226232920100
2.93-3.150.18872850.16926412926100
3.15-3.470.17813100.155726772987100
3.47-3.970.17812690.13926592928100
3.97-50.14342980.124526672965100
5-46.340.18012900.166427253015100

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