8G1E | pdb_00008g1e

Structure of ACLY-D1026A-products-asym

PDB DOI: https://doi.org/10.2210/pdb8G1E/pdb
EM Map EMD-29668: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-02-02 Released: 2023-05-10
Deposition Author(s): Wei, X., Marmorstein, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Allosteric role of the citrate synthase homology domain of ATP citrate lyase.

Wei, X., Schultz, K., Pepper, H.L., Megill, E., Vogt, A., Snyder, N.W., Marmorstein, R.

(2023) Nat Commun 14: 2247-2247

PubMed: 37076498 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-37986-9
Primary Citation Related Structures:
7RIG, 7RKZ, 7RMP, 8G1E, 8G1F, 8G5C, 8G5D

PubMed Abstract:
ATP citrate lyase (ACLY) is the predominant nucleocytosolic source of acetyl-CoA and is aberrantly regulated in many diseases making it an attractive therapeutic target. Structural studies of ACLY reveal a central homotetrameric core citrate synthase homology (CSH) module flanked by acyl-CoA synthetase homology (ASH) domains, with ATP and citrate binding the ASH domain and CoA binding the ASH-CSH interface to produce acetyl-CoA and oxaloacetate products. The specific catalytic role of the CSH module and an essential D1026A residue contained within it has been a matter of debate. Here, we report biochemical and structural analysis of an ACLY-D1026A mutant demonstrating that this mutant traps a (3S)-citryl-CoA intermediate in the ASH domain in a configuration that is incompatible with the formation of acetyl-CoA, is able to convert acetyl-CoA and OAA to (3S)-citryl-CoA in the ASH domain, and can load CoA and unload acetyl-CoA in the CSH module. Together, this data support an allosteric role for the CSH module in ACLY catalysis.

Organizational Affiliation

Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.

Macromolecule Content

Total Structure Weight: 491.49 kDa
Atom Count: 32,649
Modeled Residue Count: 4,148
Deposited Residue Count: 4,404
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-citrate synthase	A, B, C, D	1,101	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53396
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q5B Query on Q5B Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain I [auth B] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain I [auth B] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain I [auth B]	I [auth B], P [auth C], T [auth D]	(3S)-citryl-Coenzyme A C₂₇ H₄₂ N₇ O₂₂ P₃ S IHVFHZGGMJDGGZ-VPXVXCNZSA-N		Interactions Focus chain I [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain I [auth B] Focus chain P [auth C] Focus chain T [auth D]
ACO Query on ACO Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain R [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain R [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], L [auth C], R [auth D]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain R [auth D]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain N [auth C] MOL2 format, chain U [auth D] MOL2 format, chain N [auth C] mmCIF format, chain U [auth D] mmCIF format, chain N [auth C]	N [auth C], U [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain N [auth C] Focus chain U [auth D] Interactions & Density Focus chain N [auth C] Focus chain U [auth D]
OAA Query on OAA Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain M [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain S [auth D] MOL2 format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain S [auth D] mmCIF format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], M [auth C], S [auth D]	OXALOACETATE ION C₄ H₃ O₅ KHPXUQMNIQBQEV-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Focus chain S [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain K [auth B] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B]	K [auth B], Q [auth C], V [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D]
UNL( Subject of Investigation/LOI) Query on UNL Download:Ideal Coordinates CCD File	H [auth B], O [auth C]	Unknown ligand NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth B] Focus chain O [auth C] Interactions & Density Focus chain H [auth B] Focus chain O [auth C]