8BPL

Aspartate transcarbamoylase mutant (N2045C, R2238C) from Chaetomium thermophilum CAD-like bound to carbamoyl phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A Tailored Strategy to Crosslink the Aspartate Transcarbamoylase Domain of the Multienzymatic Protein CAD.

Del Cano-Ochoa, F.Rubio-Del-Campo, A.Ramon-Maiques, S.

(2023) Molecules 28

  • DOI: https://doi.org/10.3390/molecules28020660
  • Primary Citation of Related Structures:  
    8BPL, 8BPS

  • PubMed Abstract: 

    CAD is a 1.5 MDa hexameric protein with four enzymatic domains responsible for initiating de novo biosynthesis of pyrimidines nucleotides: glutaminase, carbamoyl phosphate synthetase, aspartate transcarbamoylase (ATC), and dihydroorotase. Despite its central metabolic role and implication in cancer and other diseases, our understanding of CAD is poor, and structural characterization has been frustrated by its large size and sensitivity to proteolytic cleavage. Recently, we succeeded in isolating intact CAD-like particles from the fungus Chaetomium thermophilum with high yield and purity, but their study by cryo-electron microscopy is hampered by the dissociation of the complex during sample grid preparation. Here we devised a specific crosslinking strategy to enhance the stability of this mega-enzyme. Based on the structure of the isolated C. thermophilum ATC domain, we inserted by site-directed mutagenesis two cysteines at specific locations that favored the formation of disulfide bridges and covalent oligomers. We further proved that this covalent linkage increases the stability of the ATC domain without damaging the structure or enzymatic activity. Thus, we propose that this cysteine crosslinking is a suitable strategy to strengthen the contacts between subunits in the CAD particle and facilitate its structural characterization.


  • Organizational Affiliation

    Instituto de Biomedicina de Valencia (IBV), CSIC, Jaime Roig 11, 46010 Valencia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbamoyl-phosphate synthase (glutamine-hydrolyzing)316Thermochaetoides thermophilaMutation(s): 2 
Gene Names: CTHT_0032600
UniProt
Find proteins for G0S583 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S583 
Go to UniProtKB:  G0S583
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S583
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CP (Subject of Investigation/LOI)
Query on CP

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
C H4 N O5 P
FFQKYPRQEYGKAF-UHFFFAOYSA-N
SIN
Query on SIN

Download Ideal Coordinates CCD File 
I [auth A]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.41α = 90
b = 139.41β = 90
c = 139.41γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainRTI2018-098084-B-I00
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2021-128468NB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-01
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description