4EKN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4996 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 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 68: 527-534

  • DOI: 10.1107/S1744309112011037

  • 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 crys ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate carbamoyltransferase
B
306Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: pyrB
EC: 2.1.3.2
Find proteins for Q58976 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58976
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4996 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.183 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 96.960α = 90.00
b = 96.960β = 90.00
c = 136.439γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
CBASSdata collection
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-04-09 
  • Released Date: 2012-05-09 
  • Deposition Author(s): Vitali, J.

Revision History 

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2012-06-27
    Type: Database references