Structure of the carbamate kinase-like carbamoyl phosphate synthetase from the hyperthermophilic archaeon Pyrococcus furiosus bound to ADP

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 

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The 1.5-A Resolution Crystal Structure of the Carbamate Kinase-Like Carbamoyl Phosphate Synthetase from the Hyperthermophilic Archaeon Pyrococcus Furiosus, Bound to Adp, Confirms that This Thermoestable Enzyme is a Carbamate Kinase, and Provides Insights Into Substrate Binding and Stability in Carbamate Kinases

Ramon-Maiques, S.Marina, A.Uriarte, M.Fita, I.Rubio, V.

(2000) J Mol Biol 299: 463

  • DOI: https://doi.org/10.1006/jmbi.2000.3779
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Carbamoyl phosphate (CP), an essential precursor of arginine and the pyrimidine bases, is synthesized by CP synthetase (CPS) in three steps. The last step, the phosphorylation of carbamate, is also catalyzed by carbamate kinase (CK), an enzyme used by microorganisms to produce ATP from ADP and CP. Although the recently determined structures of CPS and CK show no obvious mutual similarities, a CK-like CPS reported in hyperthermophilic archaea was postulated to be a missing link in the evolution of CP biosynthesis. The 1.5 A resolution structure of this enzyme from Pyrococcus furiosus shows both a subunit topology and a homodimeric molecular organization, with a 16-stranded open beta-sheet core surrounded by alpha-helices, similar to those in CK. However, the pyrococcal enzyme exhibits many solvent-accessible ion-pairs, an extensive, strongly hydrophobic, intersubunit surface, and presents a bound ADP molecule, which does not dissociate at 22 degrees C from the enzyme. The ADP nucleotide is sequestered in a ridge formed over the C-edge of the core sheet, at the bottom of a large cavity, with the purine ring enclosed in a pocket specific for adenine. Overall, the enzyme structure is ill-suited for catalyzing the characteristic three-step reaction of CPS and supports the view that the CK-like CPS is in fact a highly thermostable and very slow (at 37 degrees C) CK that, in the extreme environment of P. furiosus, may have the new function of making, rather than using, CP. The thermostability of the enzyme may result from the extension of the hydrophobic intersubunit contacts and from the large number of exposed ion-pairs, some of which form ion-pair networks across several secondary structure elements in each enzyme subunit. The structure provides the first information on substrate binding and catalysis in CKs, and suggests that the slow rate at 37 degrees C is possibly a consequence of slow product dissociation.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
314Pyrococcus furiosusMutation(s): 0 
Find proteins for P95474 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore P95474 
Go to UniProtKB:  P95474
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95474
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.4α = 90
b = 91.7β = 90
c = 133.8γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-04
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2023-12-06
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description