Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 328.92 kDa 
• Atom Count: 21866 
• Residue Count: 2703 
• Unique protein chains: 1

5DOT

Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), apo form

• DOI: 10.2210/pdb5DOT/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-09-11 Released: 2015-12-09 
• Deposition Author(s): Polo, L.M., de Cima, S., Fita, I., Rubio, V.
• Funding Organization(s): Fundacion Alicia Koplowitz, Valencian Government, Spanish Government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.196 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis.

de Cima, S., Polo, L.M., Diez-Fernandez, C., Martinez, A.I., Cervera, J., Fita, I., Rubio, V.

(2015) Sci Rep 5: 16950-16950

• PubMed: 26592762 
• DOI: 10.1038/srep16950
• Primary Citation of Related Structures:  
  5DOU, 5DOT


• PubMed Abstract: 
  

Human carbamoyl phosphate synthetase (CPS1), a 1500-residue multidomain enzyme, catalyzes the first step of ammonia detoxification to urea requiring N-acetyl-L-glutamate (NAG) as essential activator to prevent ammonia/amino acids depletion. Here we present the crystal structures of CPS1 in the absence and in the presence of NAG, clarifying the on/off-switching of the urea cycle by NAG. By binding at the C-terminal domain of CPS1, NAG triggers long-range conformational changes affecting the two distant phosphorylation domains. These changes, concerted with the binding of nucleotides, result in a dramatic remodeling that stabilizes the catalytically competent conformation and the building of the ~35 Å-long tunnel that allows migration of the carbamate intermediate from its site of formation to the second phosphorylation site, where carbamoyl phosphate is produced. These structures allow rationalizing the effects of mutations found in patients with CPS1 deficiency (presenting hyperammonemia, mental retardation and even death), as exemplified here for some mutations.

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Organizational Affiliation: 

Group 739, Centro de Investigación Biomédica en Red Sobre Enfermedades Raras del Instituto de Salud Carlos III (CIBERER-ISCIII), Jaime Roig 11, 46010 Valencia, Spain.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbamoyl-phosphate synthase [ammonia], mitochondrial	A, B	1489	Homo sapiens	Mutation(s): 0  Gene Names: CPS1 EC: 6.3.4.16
Find proteins for P31327 (Homo sapiens) Explore P31327  Go to UniProtKB:  P31327
NIH Common Fund Data Resources
PHAROS:  P31327 GTEx:  ENSG00000021826

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	A, B	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	A, B	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.196 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.337	α = 90
b = 133.482	β = 102.51
c = 142.907	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
XSCALE	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-09-11 
• Released Date: 2015-12-09 
Deposition Author(s): Polo, L.M., de Cima, S., Fita, I., Rubio, V.

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Funding Organization	Location	Grant Number
Fundacion Alicia Koplowitz	Spain	No grant number
Valencian Government	Spain	Prometeo 2009/051
Spanish Government	Spain	BFU2011-30407

Revision History 

• Version 1.0: 2015-12-09
  Type: Initial release