4C6M

Crystal structure of the dihydroorotase domain of human CAD bound to the inhibitor fluoroorotate at pH 7.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.115 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure, Functional Characterization and Evolution of the Dihydroorotase Domain of Human Cad.

Grande-Garcia, A.Lallous, N.Diaz-Tejada, C.Ramon-Maiques, S.

(2014) Structure 22: 185

  • DOI: 10.1016/j.str.2013.10.016
  • Primary Citation of Related Structures:  
    4C6B, 4C6C, 4C6D, 4C6E, 4C6F, 4C6O, 4C6P, 4C6Q, 4C6I, 4C6J

  • PubMed Abstract: 
  • Upregulation of CAD, the multifunctional protein that initiates and controls the de novo biosynthesis of pyrimidines in animals, is essential for cell proliferation. Deciphering the architecture and functioning of CAD is of interest for its potential usa ...

    Upregulation of CAD, the multifunctional protein that initiates and controls the de novo biosynthesis of pyrimidines in animals, is essential for cell proliferation. Deciphering the architecture and functioning of CAD is of interest for its potential usage as an antitumoral target. However, there is no detailed structural information about CAD other than that it self-assembles into hexamers of ∼1.5 MDa. Here we report the crystal structure and functional characterization of the dihydroorotase domain of human CAD. Contradicting all assumptions, the structure reveals an active site enclosed by a flexible loop with two Zn²⁺ ions bridged by a carboxylated lysine and a third Zn coordinating a rare histidinate ion. Site-directed mutagenesis and functional assays prove the involvement of the Zn and flexible loop in catalysis. Comparison with homologous bacterial enzymes supports a reclassification of the DHOase family and provides strong evidence against current models of the architecture of CAD.


    Organizational Affiliation

    Structural Bases of Genome Integrity Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain. Electronic address: sramon@cnio.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAD PROTEIN A393Homo sapiensMutation(s): 0 
Gene Names: CAD
EC: 3.5.2.3 (PDB Primary Data), 6.3.5.5 (UniProt), 2.1.3.2 (UniProt)
Find proteins for P27708 (Homo sapiens)
Explore P27708 
Go to UniProtKB:  P27708
NIH Common Fund Data Resources
PHAROS:  P27708
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FOT
Query on FOT

Download Ideal Coordinates CCD File 
A
5-FLUORO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID
C5 H3 F N2 O4
SEHFUALWMUWDKS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
AL-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.113 
  • R-Value Observed: 0.115 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.25α = 90
b = 158.64β = 90
c = 61.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-02-19
    Changes: Database references