8Z03 | pdb_00008z03

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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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 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.

Macromolecule Content 

  • Total Structure Weight: 77.85 kDa 
  • Atom Count: 5,493 
  • Modeled Residue Count: 704 
  • Deposited Residue Count: 716 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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), 6.2.1.9 (UniProt), 6.2.1 (UniProt)
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:|  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 (PDB Primary Data), 6.2.1 (UniProt)
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 


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