Aspartate transcarbamoylase domain of human CAD bound to PALA

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 

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Structure and Functional Characterization of Human Aspartate Transcarbamoylase, the Target of the Anti-Tumoral Drug Pala.

Ruiz-Ramos, A.Velazquez-Campoy, A.Grande-Garcia, A.Moreno-Morcillo, M.Ramon-Maiques, S.

(2016) Structure 24: 1081

  • DOI: https://doi.org/10.1016/j.str.2016.05.001
  • Primary Citation of Related Structures:  
    5G1N, 5G1O, 5G1P

  • PubMed Abstract: 

    CAD, the multienzymatic protein that initiates and controls de novo synthesis of pyrimidines in animals, associates through its aspartate transcarbamoylase (ATCase) domain into particles of 1.5 MDa. Despite numerous structures of prokaryotic ATCases, we lack structural information on the ATCase domain of CAD. Here, we report the structure and functional characterization of human ATCase, confirming the overall similarity with bacterial homologs. Unexpectedly, human ATCase exhibits cooperativity effects that reduce the affinity for the anti-tumoral drug PALA. Combining structural, mutagenic, and biochemical analysis, we identified key elements for the necessary regulation and transmission of conformational changes leading to cooperativity between subunits. Mutation of one of these elements, R2024, was recently found to cause the first non-lethal CAD deficit. We reproduced this mutation in human ATCase and measured its effect, demonstrating that this arginine is part of a molecular switch that regulates the equilibrium between low- and high-affinity states for the ligands.

  • Organizational Affiliation

    Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fdez. Almagro, 3, Madrid 28029, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
314Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P27708 (Homo sapiens)
Explore P27708 
Go to UniProtKB:  P27708
PHAROS:  P27708
GTEx:  ENSG00000084774 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27708
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PAL Binding MOAD:  5G1N Kd: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.03α = 90
b = 145.12β = 120.03
c = 83.16γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references, Structure summary
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description