8Z03

Lactate bound to human GTP-specific succinyl-CoA synthetase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.244 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted COAClick on this verticalbar to view detailsBest fitted PO4Click on this verticalbar to view detailsBest fitted 2OPClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and gliomagenesis.

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.

(2025) Cell Metab 37: 377

  • DOI: https://doi.org/10.1016/j.cmet.2024.11.005
  • Primary Citation of Related Structures:  
    8Z02, 8Z03

  • PubMed Abstract: 

    Histone lysine lactylation is a physiologically and pathologically relevant epigenetic pathway that can be stimulated by the Warburg effect-associated L-lactate. Nevertheless, the mechanism by which cells use L-lactate to generate lactyl-coenzyme A (CoA) and how this process is regulated remains unknown. Here, we report the identification of guanosine triphosphate (GTP)-specific SCS (GTPSCS) as a lactyl-CoA synthetase in the nucleus. The mechanism was elucidated through the crystallographic structure of GTPSCS in complex with L-lactate, followed by mutagenesis experiments. GTPSCS translocates into the nucleus and interacts with p300 to elevate histone lactylation but not succinylation. This process depends on a nuclear localization signal in the GTPSCS G1 subunit and acetylation at G2 subunit residue K73, which mediates the interaction with p300. GTPSCS/p300 collaboration synergistically regulates histone H3K18la and GDF15 expression, promoting glioma proliferation and radioresistance. GTPSCS represents the inaugural enzyme to catalyze lactyl-CoA synthesis for epigenetic histone lactylation and regulate oncogenic gene expression in glioma.


  • Organizational Affiliation

    State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA; Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial321Homo sapiensMutation(s): 0 
Gene Names: SUCLG1
EC: 6.2.1.4 (PDB Primary Data), 6.2.1.5 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P53597 (Homo sapiens)
Explore P53597 
Go to UniProtKB:  P53597
PHAROS:  P53597
GTEx:  ENSG00000163541 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53597
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial395Homo sapiensMutation(s): 0 
Gene Names: SUCLG2
EC: 6.2.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96I99 (Homo sapiens)
Explore Q96I99 
Go to UniProtKB:  Q96I99
PHAROS:  Q96I99
GTEx:  ENSG00000172340 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96I99
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.244 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.12α = 90
b = 134.37β = 92.13
c = 57.83γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted COAClick on this verticalbar to view detailsBest fitted PO4Click on this verticalbar to view detailsBest fitted 2OPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM135504
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA251677
National Natural Science Foundation of China (NSFC)China81973164

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references
  • Version 1.2: 2025-02-19
    Changes: Database references