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- PDB-7msr: Human E105Qa GTP-specific succinyl-CoA synthetase complexed with ... -

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Basic information

Entry
Database: PDB / ID: 7msr
TitleHuman E105Qa GTP-specific succinyl-CoA synthetase complexed with succinyl-phosphate, magnesium ion and desulfo-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 / succinyl-CoA catabolic process / succinyl-CoA metabolic process / succinate 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 / succinyl-CoA catabolic process / succinyl-CoA metabolic process / succinate metabolic process / Citric acid cycle (TCA cycle) / tricarboxylic acid cycle / Mitochondrial protein degradation / GDP binding / mitochondrial matrix / nucleotide binding / GTP binding / protein-containing complex 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 / 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. ...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 / 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 / ATP-grasp fold, subdomain 1 / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DESULFO-COENZYME A / 4-oxo-4-(phosphonooxy)butanoic acid / 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: 1.58 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)77,54210
Polymers76,1542
Non-polymers1,3888
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-24 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.436, 81.452, 54.331
Angle α, β, γ (deg.)90.000, 103.370, 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: 33526.363 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 / GTPSCS / Succinyl-CoA synthetase beta-G chain / SCS-betaG


Mass: 42627.781 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 , 6 types, 307 molecules

#3: Chemical ChemComp-DCA / DESULFO-COENZYME A


Mass: 735.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-ZNS / 4-oxo-4-(phosphonooxy)butanoic acid


Mass: 198.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7O7P / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 45.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 22.5% (w/v) PEG3350, 100 mM ammonium succinate pH 7.5, 100 mM Tris-HCl pH 7.4

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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: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→56.43 Å / Num. obs: 92537 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.16 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.071 / Net I/σ(I): 9.5 / Num. measured all: 320245
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.58-1.613.40.31520644861.1312.11796.4
4.29-56.473.747.81762047850.020.04100

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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: 6XRU

6xru


Resolution: 1.58→39.13 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 6027 6.62 %
Rwork0.1987 84954 -
obs0.2007 90981 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126 Å2 / Biso mean: 40.8869 Å2 / Biso min: 15.23 Å2
Refinement stepCycle: final / Resolution: 1.58→39.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 164 299 5707
Biso mean--40.58 40.91 -
Num. residues----700
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 (%)
1.58-1.60.4661860.43252008209467
1.6-1.620.44291300.41322486261686
1.62-1.640.41231430.39772766290992
1.64-1.660.39341360.37252892302897
1.66-1.680.3451410.35982874301598
1.68-1.70.36441370.34452932306998
1.7-1.730.37891720.32642822299499
1.73-1.750.32971190.31342983310298
1.75-1.780.3451370.32062914305199
1.78-1.810.32311660.31452903306999
1.81-1.840.28381160.30642935305199
1.84-1.870.31631430.28382959310299
1.87-1.910.27831360.2652899303599
1.91-1.950.27631520.24252936308899
1.95-1.990.27341490.23292911306099
1.99-2.040.24411600.22332947310799
2.04-2.090.27331400.21962935307599
2.09-2.140.23971760.211628943070100
2.14-2.210.23891960.207429023098100
2.21-2.280.242450.208128783123100
2.28-2.360.23872760.214828193095100
2.36-2.450.23883010.196827953096100
2.45-2.570.23083200.194727843104100
2.57-2.70.25173170.195527903107100
2.7-2.870.22992980.189728293127100
2.87-3.090.2382900.192428063096100
3.09-3.40.20873220.177328143136100
3.4-3.90.20113180.162328123130100
3.9-4.910.16543070.137928283135100
4.91-39.130.20132980.171429013199100

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