2W37

CRYSTAL STRUCTURE OF THE HEXAMERIC CATABOLIC ORNITHINE TRANSCARBAMYLASE FROM Lactobacillus hilgardii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Hexameric Catabolic Ornithine Transcarbamylase from Lactobacillus Hilgardii: Structural Insights Into the Oligomeric Assembly and Metal Binding.

De Las Rivas, B.Fox, G.C.Angulo, I.Ripoll, M.M.Rodriguez, H.Munoz, R.Mancheno, J.M.

(2009) J.Mol.Biol. 393: 425

  • DOI: 10.1016/j.jmb.2009.08.002

  • PubMed Abstract: 
  • Catabolic ornithine transcarbamylase (cOTC; EC 2.1.3.3) catalyzes the formation of ornithine (ORN) and carbamoyl phosphate from citrulline, which constitutes the second step of the degradation of arginine via the arginine deiminase pathway. Here, we ...

    Catabolic ornithine transcarbamylase (cOTC; EC 2.1.3.3) catalyzes the formation of ornithine (ORN) and carbamoyl phosphate from citrulline, which constitutes the second step of the degradation of arginine via the arginine deiminase pathway. Here, we report the crystal structure of cOTC from the lactic acid bacteria Lactobacillus hilgardii (Lh-cOTC) refined to 2.1 A resolution. The structure reveals that Lh-cOTC forms a hexameric assembly, which was also confirmed by gel-filtration chromatography and analytical ultracentrifugation. The homohexamer, with 32 point group symmetry, represents a new oligomeric state within the members of the ornithine transcarbamylase family that are typically homotrimeric or homododecameric. The C-terminal end from each subunit constitutes a key structural element for the stabilization of the hexameric assembly in solution. Additionally, the structure reveals, for the first time in the ornithine transcarbamylase family, a metal-binding site located at the 3-fold molecular symmetry axis of each trimer.


    Organizational Affiliation

    Departamento de MicrobiologĂ­a, Instituto de Fermentaciones Industriales, CSIC, Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ORNITHINE CARBAMOYLTRANSFERASE, CATABOLIC
A, B, C
359Lactobacillus hilgardiiMutation(s): 0 
Gene Names: arcB
EC: 2.1.3.3
Find proteins for Q8G998 (Lactobacillus hilgardii)
Go to UniProtKB:  Q8G998
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.196 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 156.805α = 90.00
b = 156.805β = 90.00
c = 80.623γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance