4EKN

Structure of the catalytic chain of Methanococcus jannaschii Aspartate Transcarbamoylase in a hexagonal crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.192 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structure of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase in a hexagonal crystal form: insights into the path of carbamoyl phosphate to the active site of the enzyme.

Vitali, J.Singh, A.K.Soares, A.S.Colaneri, M.J.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 527-534

  • DOI: https://doi.org/10.1107/S1744309112011037
  • Primary Citation of Related Structures:  
    4EKN

  • PubMed Abstract: 

    Crystals of the catalytic chain of Methanococcus jannaschii aspartate transcarbamoylase (ATCase) grew in the presence of the regulatory chain in the hexagonal space group P6(3)22, with one monomer per asymmetric unit. This is the first time that crystals with only one monomer in the asymmetric unit have been obtained; all known structures of the catalytic subunit contain several crystallographically independent monomers. The symmetry-related chains form the staggered dimer of trimers observed in the other known structures of the catalytic subunit. The central channel of the catalytic subunit contains a sulfate ion and a K(+) ion as well as a glycerol molecule at its entrance. It is possible that it is involved in channeling carbamoyl phosphate (CP) to the active site of the enzyme. A second sulfate ion near Arg164 is near the second CP position in the wild-type Escherichia coli ATCase structure complexed with CP. It is suggested that this position may also be in the path that CP takes when binding to the active site in a partial diffusion process at 310 K. Additional biochemical studies of carbamoylation and the molecular organization of this enzyme in M. jannaschii will provide further insight into these points.


  • Organizational Affiliation

    Department of Physics, Cleveland State University, Euclid Avenue at East 24th Street, Cleveland, OH 44115, USA. j.vitali@csuohio.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate carbamoyltransferaseA [auth B]306Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: MJ1581pyrB
EC: 2.1.3.2
UniProt
Find proteins for Q58976 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58976 
Go to UniProtKB:  Q58976
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58976
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.192 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.96α = 90
b = 96.96β = 90
c = 136.439γ = 120
Software Package:
Software NamePurpose
CBASSdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2012-05-09 
  • Deposition Author(s): Vitali, J.

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2012-06-27
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description