6UUW

Structure of human ATP citrate lyase E599Q mutant in complex with Mg2+, citrate, ATP and CoA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

Molecular basis for acetyl-CoA production by ATP-citrate lyase

Wei, X.Schultz, K.Bazilevsky, G.A.Vogt, A.Marmorstein, R.

(2020) Nat Struct Mol Biol 27: 33-41

  • DOI: https://doi.org/10.1038/s41594-019-0351-6
  • Primary Citation of Related Structures:  
    6POE, 6POF, 6UI9, 6UIA, 6UUW, 6UUZ, 6UV5

  • PubMed Abstract: 

    ATP-citrate lyase (ACLY) synthesizes cytosolic acetyl coenzyme A (acetyl-CoA), a fundamental cellular building block. Accordingly, aberrant ACLY activity is observed in many diseases. Here we report cryo-EM structures of human ACLY, alone or bound to substrates or products. ACLY forms a homotetramer with a rigid citrate synthase homology (CSH) module, flanked by four flexible acetyl-CoA synthetase homology (ASH) domains; CoA is bound at the CSH-ASH interface in mutually exclusive productive or unproductive conformations. The structure of a catalytic mutant of ACLY in the presence of ATP, citrate and CoA substrates reveals a phospho-citryl-CoA intermediate in the ASH domain. ACLY with acetyl-CoA and oxaloacetate products shows the products bound in the ASH domain, with an additional oxaloacetate in the CSH domain, which could function in ACLY autoinhibition. These structures, which are supported by biochemical and biophysical data, challenge previous proposals of the ACLY catalytic mechanism and suggest additional therapeutic possibilities for ACLY-associated metabolic disorders.


  • Organizational Affiliation

    Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-citrate synthase
A, B, C, D
1,101Homo sapiensMutation(s): 1 
Gene Names: ACLY
EC: 2.3.3.8
UniProt & NIH Common Fund Data Resources
Find proteins for P53396 (Homo sapiens)
Explore P53396 
Go to UniProtKB:  P53396
PHAROS:  P53396
GTEx:  ENSG00000131473 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53396
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
M [auth C],
Q [auth D]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
P [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Y2A (Subject of Investigation/LOI)
Query on Y2A

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
N [auth C],
R [auth D]
(2S)-2-hydroxy-2-[2-oxo-2-(phosphonooxy)ethyl]butanedioic acid
C6 H9 O10 P
RAAPFOXFYNTKEB-LURJTMIESA-N
UNL
Query on UNL

Download Ideal Coordinates CCD File 
H [auth A],
O [auth C]
Unknown ligand
RAAPFOXFYNTKEB-LURJTMIESA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references, Structure summary
  • Version 1.2: 2020-01-22
    Changes: Database references
  • Version 2.0: 2020-02-19
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2021-08-11
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary