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 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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: https://doi.org/10.1038/srep16950
  • Primary Citation of 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.


  • Organizational Affiliation

    Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaime Roig 11, 46010 Valencia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbamoyl-phosphate synthase [ammonia], mitochondrial
A, B
1,489Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31327
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth A],
L [auth B],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
H [auth A],
K [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
C [auth A],
J [auth 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 = 99.337α = 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  (Full details and data files)

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