6NZY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

  • DOI: 10.1002/pro.3708

  • 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 us ...

    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

    Structural Biology Unit, CSIC, Barcelona, Spain.,Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.,ICREA, Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-citrate lyase alpha-subunit
A, B, C, D
262Chlorobium limicolaMutation(s): 0 
Gene Names: aclA
Find proteins for Q9AJC4 (Chlorobium limicola)
Go to UniProtKB:  Q9AJC4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACO
Query on ACO

Download SDF File 
Download CCD File 
A, D
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.167 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 82.180α = 90.00
b = 82.180β = 90.00
c = 151.200γ = 120.00
Software Package:
Software NamePurpose
DIALSdata reduction
PHENIXrefinement
DIALSdata scaling
Arcimboldophasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada222915-2013

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release