6NZY | pdb_00006nzy

Structural Determination of the Carboxy-terminal portion of ATP-citrate lyase

PDB DOI: https://doi.org/10.2210/pdb6NZY/pdb

Classification: LYASE
Organism(s): Chlorobium limicola
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-02-14 Released: 2019-12-18
Deposition Author(s): Nguyen, V.H., Fraser, M.E.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.190 (Depositor), 0.176 (DCC)
R-Value Work:
0.167 (Depositor)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Identification of the active site residues in ATP-citrate lyase's carboxy-terminal portion.

Nguyen, V.H., Singh, N., Medina, A., Uson, I., Fraser, M.E.

(2019) Protein Sci 28: 1840-1849

PubMed: 31411782 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.3708
Primary Citation Related Structures:
6NZY

PubMed Abstract:
ATP-citrate lyase (ACLY) catalyzes production of acetyl-CoA and oxaloacetate from CoA and citrate using ATP. In humans, this cytoplasmic enzyme connects energy metabolism from carbohydrates to the production of lipids. In certain bacteria, ACLY is used to fix carbon in the reductive tricarboxylic acid cycle. The carboxy(C)-terminal portion of ACLY shows sequence similarity to citrate synthase of the tricarboxylic acid cycle. To investigate the roles of residues of ACLY equivalent to active site residues of citrate synthase, these residues in ACLY from Chlorobium limicola were mutated, and the proteins were investigated using kinetics assays and biophysical techniques. To obtain the crystal structure of the C-terminal portion of ACLY, full-length C. limicola ACLY was cleaved, first non-specifically with chymotrypsin and subsequently with Tobacco Etch Virus protease. Crystals of the C-terminal portion diffracted to high resolution, providing structures that show the positions of active site residues and how ACLY tetramerizes.

Organizational Affiliation

Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

Macromolecule Content

Total Structure Weight: 118.88 kDa
Atom Count: 8,564
Modeled Residue Count: 1,035
Deposited Residue Count: 1,048
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-citrate lyase alpha-subunit	A, B, C, D	262	Chlorobium limicola	Mutation(s): 0 Gene Names: aclA
UniProt
Find proteins for Q9AJC4 (Chlorobium limicola) Explore Q9AJC4 Go to UniProtKB: Q9AJC4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9AJC4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO Query on ACO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain Y [auth D]	E [auth A], Y [auth D]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain E [auth A] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain Y [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain F [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	F [auth A], R [auth B], T [auth C], Z [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain R [auth B] Focus chain T [auth C] Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] G [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], U [auth C], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth C] Focus chain V [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain S [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	EA [auth D] FA [auth D] O [auth A] P [auth A] Q [auth A] EA [auth D], FA [auth D], O [auth A], P [auth A], Q [auth A], S [auth B], W [auth C], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain FA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain FA [auth D] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.190 (Depositor), 0.176 (DCC)
R-Value Work: 0.167 (Depositor)
R-Value Observed: 0.168 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.18	α = 90
b = 82.18	β = 90
c = 151.2	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
Arcimboldo	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Nguyen, V.H.

Fraser, M.E.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	222915-2013

Revision History (Full details and data files)

Version 1.0: 2019-12-18
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description