5DOT

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


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 

wwPDB Validation   3D Report Full Report



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

  • 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 prese ...

    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.


    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbamoyl-phosphate synthase [ammonia], mitochondrial AB1489Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
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 = 99.337α = 90
b = 133.482β = 102.51
c = 142.907γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacion Alicia KoplowitzSpainNo grant number
Valencian GovernmentSpainPrometeo 2009/051
Spanish GovernmentSpainBFU2011-30407

Revision History 

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