9FS2 | pdb_00009fs2

Mutant S1538A of the dihydroorotase domain of human CAD protein bound to substrate

• PDB DOI: https://doi.org/10.2210/pdb9FS2/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-06-20 Released: 2024-12-04 
• Deposition Author(s): del Cano-Ochoa, F., Ramon-Maiques, S.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN), Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.169 (Depositor) 
• R-Value Work: 
  0.147 (Depositor) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Disruption of CAD Oligomerization by Pathogenic Variants.

Del Cano-Ochoa, F., Ramadane-Morchadi, L., Eixeres, L., Moreno-Morcillo, M., Fernandez-Leiro, R., Ramon-Maiques, S.

(2024) J Mol Biology 436: 168832-168832

• PubMed: 39447673 
• DOI: https://doi.org/10.1016/j.jmb.2024.168832
• Primary Citation Related Structures: 
  9FS1, 9FS2, 9FS3


• PubMed Abstract: 
  

  CAD, the multi-enzymatic protein essential for initiating the de novo biosynthesis of pyrimidine nucleotides, forms large hexamers whose structure and function are not fully understood. Defects in CAD cause a severe neurometabolic disorder that is challenging to diagnose. We developed a cellular functional assay to identify defective CAD variants, and in this study, we characterized five pathogenic missense mutations in CAD's dihydroorotase (DHO) and aspartate transcarbamoylase (ATC) domains. All mutations impaired enzymatic activities, with two notably disrupting the formation of DHO dimers and ATC trimers. Combining crystal structures and AlphaFold predictions, we modeled the hexameric CAD complex, highlighting the central role of the DHO and ATC domains in its assembly. Our findings provide insight into CAD's stability, function, and organization, revealing that correct oligomerization of CAD into a supramolecular complex is required for its function in nucleotide synthesis and that mutations affecting this assembly are potentially pathogenic.

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Organizational Affiliation: 
• Structure of Macromolecular Targets Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Eduardo Primo Yúfera, 3, 46012 Valencia, Spain. Electronic address: [e-mail].
Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Prof Marín Lagos, S/N, 28040 Moncloa-Aravaca, Madrid, Spain.
Structure of Macromolecular Targets Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Eduardo Primo Yúfera, 3, 46012 Valencia, Spain.
Genome Integrity and Structural Biology Group, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, 28029 Madrid, Spain.
Structure of Macromolecular Targets Unit, Instituto de Biomedicina de Valencia (IBV), CSIC, Eduardo Primo Yúfera, 3, 46012 Valencia, Spain; Group CB06/07/0077 Centro de Investigación Biomédica en Red de Enfermedades Raras, CIBERER-ISCIII, Monforte de Lemos 3-5, 28029 Madrid, Spain; Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF) - Associated Unit to the Instituto de Biomedicina de Valencia (IBV), Eduardo Primo Yúfera, 3, 46012 Valencia, Spain. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.78 kDa 
• Atom Count: 3,526 
• Modeled Residue Count: 362 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multifunctional protein CAD	A	362	Homo sapiens	Mutation(s): 1  Gene Names: CAD EC: 6.3.5.5 (PDB Primary Data), 3.5.1.2 (PDB Primary Data), 6.3.4.16 (PDB Primary Data), 2.1.3.2 (PDB Primary Data), 3.5.2.3 (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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCD (Subject of Investigation/LOI)	D [auth A]	N-CARBAMOYL-L-ASPARTATE C5 H8 N2 O5 HLKXYZVTANABHZ-REOHCLBHSA-N
DOR (Subject of Investigation/LOI)	F [auth A]	(4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID C5 H6 N2 O4 UFIVEPVSAGBUSI-REOHCLBHSA-N
ZN	B [auth A], C [auth A], E [auth A], N [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free:  0.169 (Depositor) 
• R-Value Work:  0.147 (Depositor) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.142	α = 90
b = 158.579	β = 90
c = 61.95	γ = 90

Software Package:

Software Name	Purpose
EDNA	data collection
autoPROC	data processing
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): del Cano-Ochoa, F., Ramon-Maiques, S.

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Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2021-128468NB-I00
Other private		Fundacion Ramon Areces

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release