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- PDB-8z03: Lactate bound to human GTP-specific succinyl-CoA synthetase -

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Basic information

Entry
Database: PDB / ID: 8z03
TitleLactate bound to human GTP-specific succinyl-CoA synthetase
Components(Succinate--CoA ligase ...) x 2
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
(2S)-2-HYDROXYPROPANOIC ACID / 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: 1.99 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)77,8556
Polymers76,8782
Non-polymers9774
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-43 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.120, 134.370, 57.830
Angle α, β, γ (deg.)90.000, 92.130, 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: 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)

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Non-polymers , 5 types, 218 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M TRIS pH=7.5, 20% w/v PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.99→43.81 Å / Num. obs: 55815 / % possible obs: 99 % / Redundancy: 5.1 % / CC1/2: 0.986 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.087 / Rrim(I) all: 0.201 / Net I/σ(I): 6.6 / Num. measured all: 286049 / Scaling rejects: 432
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
1.99-2.045.30.8722184741090.7010.410.9652.298.7
8.9-43.815.20.09132766300.9840.0440.10114.697.1

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cae

5cae


Resolution: 1.99→42.129 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 2806 5.03 %
Rwork0.2072 52967 -
obs0.209 55773 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.55 Å2 / Biso mean: 23.8282 Å2 / Biso min: 10.46 Å2
Refinement stepCycle: final / Resolution: 1.99→42.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5219 0 60 214 5493
Biso mean--20.25 24.89 -
Num. residues----704
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.99-2.02430.33811380.268260198
2.0243-2.06110.27131490.253266599
2.0611-2.10080.29161710.2367258898
2.1008-2.14370.33081440.2315264299
2.1437-2.19030.30191440.2185261098
2.1903-2.24120.24951640.2154266199
2.2412-2.29730.26361410.2132262199
2.2973-2.35940.2731620.2164264198
2.3594-2.42880.24991430.21292638100
2.4288-2.50720.28571040.2132268599
2.5072-2.59680.26621120.2146267399
2.5968-2.70070.28011310.2176268699
2.7007-2.82360.24161260.2175266099
2.8236-2.97240.25011800.2202261399
2.9724-3.15860.2291420.2239264899
3.1586-3.40240.25521130.2032270299
3.4024-3.74460.251290.1956263299
3.7446-4.2860.21081010.1771269699
4.286-5.39810.18091700.1806264398
5.3981-42.1290.20781420.2004266298

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