5DOU | pdb_00005dou

Crystal Structure of Human Carbamoyl phosphate synthetase I (CPS1), ligand-bound form

• PDB DOI: https://doi.org/10.2210/pdb5DOU/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): de Cima, S., Polo, L.M., 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: 2.60 Å
• R-Value Free: 
  0.229 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1038/srep16950
• Primary Citation Related Structures: 
  5DOT, 5DOU


• 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: 
• Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaime Roig 11, 46010 Valencia, Spain.
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.
Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, 46012 Valencia, Spain.
Instituto de Biología Molecular de Barcelona del Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 662.38 kDa 
• Atom Count: 45,021 
• Modeled Residue Count: 5,699 
• Deposited Residue Count: 5,956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbamoyl-phosphate synthase [ammonia], mitochondrial	A, B, C, D	1,489	Homo sapiens	Mutation(s): 0  Gene Names: CPS1 EC: 6.3.4.16
UniProt & NIH Common Fund Data Resources
Find proteins for P31327 (Homo sapiens) Explore P31327  Go to UniProtKB:  P31327
PHAROS:  P31327 GTEx:  ENSG00000021826

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	AB [auth D], BA [auth B], BB [auth D], CA [auth B], L [auth A], M [auth A], OA [auth C], PA [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
NLG	CB [auth D], DA [auth B], N [auth A], QA [auth C]	N-ACETYL-L-GLUTAMATE C7 H11 N O5 RFMMMVDNIPUKGG-YFKPBYRVSA-N
PO4	AA [auth B], K [auth A], NA [auth C], ZA [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	HB [auth D], S [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	T [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	E [auth A], HA [auth C], TA [auth D], U [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
K	FB [auth D], GA [auth B], GB [auth D], H [auth A], I [auth A], J [auth A], KA [auth C], LA [auth C], MA [auth C], Q [auth A], R [auth A], SA [auth C], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	EB [auth D], FA [auth B], P [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	DB [auth D], EA [auth B], F [auth A], G [auth A], IA [auth C], JA [auth C], O [auth A], RA [auth C], UA [auth D], V [auth B], VA [auth D], W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.229 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.919	α = 90.66
b = 98.558	β = 98.65
c = 214.89	γ = 90.08

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description