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- PDB-8z02: CoA bound to human GTP-specific succinyl-CoA synthetase -

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Basic information

Entry
Database: PDB / ID: 8z02
TitleCoA bound to human GTP-specific succinyl-CoA synthetase
Components
  • Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
  • Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
KeywordsLIGASE / GTP-specific succinyl-CoA synthetase / GTPSCS / lactyl-CoA ligase
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 / 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 / PHOSPHATE ION / 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: 2.32 Å
AuthorsLiu, R.L. / Ren, X.L. / Li, L.T. / Zhang, Y. / Huang, H. / Zhao, Y.M.
Funding support United States, China, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135504 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA251677 United States
National Natural Science Foundation of China (NSFC)81973164 China
CitationJournal: Cell Metab. / Year: 2025
Title: Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and gliomagenesis.
Authors: Liu, R. / Ren, X. / Park, Y.E. / Feng, H. / Sheng, X. / Song, X. / AminiTabrizi, R. / Shah, H. / Li, L. / Zhang, Y. / Abdullah, K.G. / Dubois-Coyne, S. / Lin, H. / Cole, P.A. / DeBerardinis, ...Authors: Liu, R. / Ren, X. / Park, Y.E. / Feng, H. / Sheng, X. / Song, X. / AminiTabrizi, R. / Shah, H. / Li, L. / Zhang, Y. / Abdullah, K.G. / Dubois-Coyne, S. / Lin, H. / Cole, P.A. / DeBerardinis, R.J. / McBrayer, S.K. / Huang, H. / Zhao, Y.
History
DepositionApr 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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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)77,7404
Polymers76,8782
Non-polymers8632
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-34 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.630, 105.700, 126.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34250.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLG1 / Production host: Escherichia coli BL21(DE3) (bacteria)
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: 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)
References: UniProt: Q96I99, succinate-CoA ligase (GDP-forming)
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7, 15% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.32→48.781 Å / Num. obs: 33736 / % possible obs: 99.9 % / Redundancy: 8.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.077 / Rrim(I) all: 0.224 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.32-2.49.21.1762994032490.7070.4081.2492.299.9
8.99-48.787.20.04249016780.9980.0160.04626.999.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cae

5cae


Resolution: 2.32→48.781 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1673 4.97 %
Rwork0.2124 31978 -
obs0.2143 33651 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.66 Å2 / Biso mean: 40.9942 Å2 / Biso min: 14.65 Å2
Refinement stepCycle: final / Resolution: 2.32→48.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5199 0 53 130 5382
Biso mean--33.82 34.36 -
Num. residues----703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.32-2.38830.32631460.27942616100
2.3883-2.46540.3331350.27982639100
2.4654-2.55350.31011340.27922606100
2.5535-2.65570.31921360.27332632100
2.6557-2.77660.35681360.26032659100
2.7766-2.92290.27741350.26072633100
2.9229-3.1060.27711310.25032651100
3.106-3.34580.26621370.22962680100
3.3458-3.68240.25471380.2116263299
3.6824-4.2150.24541410.1852687100
4.215-5.30940.19841350.15882744100
5.3094-48.7810.17661690.171279999

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