Structure of citryl-CoA lyase from Hydrogenobacter thermophilus

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

Starting Model: other
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Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.

Verschueren, K.H.G.Blanchet, C.Felix, J.Dansercoer, A.De Vos, D.Bloch, Y.Van Beeumen, J.Svergun, D.Gutsche, I.Savvides, S.N.Verstraete, K.

(2019) Nature 568: 571-575

  • DOI: https://doi.org/10.1038/s41586-019-1095-5
  • Primary Citation of Related Structures:  
    6HXH, 6HXI, 6HXJ, 6HXK, 6HXL, 6HXM, 6HXN, 6HXO, 6HXP, 6HXQ, 6QCL, 6QFB

  • PubMed Abstract: 

    Across different kingdoms of life, ATP citrate lyase (ACLY, also known as ACL) catalyses the ATP-dependent and coenzyme A (CoA)-dependent conversion of citrate, a metabolic product of the Krebs cycle, to oxaloacetate and the high-energy biosynthetic precursor acetyl-CoA 1 . The latter fuels pivotal biochemical reactions such as the synthesis of fatty acids, cholesterol and acetylcholine 2 , and the acetylation of histones and proteins 3,4 . In autotrophic prokaryotes, ACLY is a hallmark enzyme of the reverse Krebs cycle (also known as the reductive tricarboxylic acid cycle), which fixates two molecules of carbon dioxide in acetyl-CoA 5,6 . In humans, ACLY links carbohydrate and lipid metabolism and is strongly expressed in liver and adipose tissue 1 and in cholinergic neurons 2,7 . The structural basis of the function of ACLY remains unknown. Here we report high-resolution crystal structures of bacterial, archaeal and human ACLY, and use distinct substrate-bound states to link the conformational plasticity of ACLY to its multistep catalytic itinerary. Such detailed insights will provide the framework for targeting human ACLY in cancer 8-11 and hyperlipidaemia 12,13 . Our structural studies also unmask a fundamental evolutionary relationship that links citrate synthase, the first enzyme of the oxidative Krebs cycle, to an ancestral tetrameric citryl-CoA lyase module that operates in the reverse Krebs cycle. This molecular transition marked a key step in the evolution of metabolism on Earth.

  • Organizational Affiliation

    Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Citryl-CoA lyase268Hydrogenobacter thermophilusMutation(s): 0 
Gene Names: ccl
Find proteins for Q75VX1 (Hydrogenobacter thermophilus)
Explore Q75VX1 
Go to UniProtKB:  Q75VX1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75VX1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.596α = 90
b = 130.596β = 90
c = 83.947γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgium1524918N

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description