4ADD

Structural and functional study of succinyl-ornithine transaminase from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Determination of the Structure of the Catabolic N-Succinylornithine Transaminase (Astc) from Escherichia Coli.

Newman, J.Seabrook, S.Surjadi, R.Williams, C.C.Lucent, D.Wilding, M.Scott, C.Peat, T.S.

(2013) Plos One 8: 58298

  • DOI: 10.1371/journal.pone.0058298
  • Primary Citation of Related Structures:  4ADB, 4ADC, 4ADE

  • PubMed Abstract: 
  • Escherichia coli possesses two acyl ornithine aminotransferases, one catabolic (AstC) and the other anabolic (ArgD), that participate in L-arginine metabolism. Although only 58% identical, the enzymes have been shown to be functionally interchangeabl ...

    Escherichia coli possesses two acyl ornithine aminotransferases, one catabolic (AstC) and the other anabolic (ArgD), that participate in L-arginine metabolism. Although only 58% identical, the enzymes have been shown to be functionally interchangeable. Here we have purified AstC and have obtained X-ray crystal structures of apo and holo-AstC and of the enzyme complexed with its physiological substrate, succinylornithine. We compare the structures obtained in this study with those of ArgD from Salmonella typhimurium obtained elsewhere, finding several notable differences. Docking studies were used to explore the docking modes of several substrates (ornithine, succinylornithine and acetylornithine) and the co-substrate glutamate/α-ketogluterate. The docking studies support our observations that AstC has a strong preference for acylated ornithine species over ornithine itself, and suggest that the increase in specificity associated with acylation is caused by steric and desolvation effects rather than specific interactions between the substrate and enzyme.


    Organizational Affiliation

    CSIRO Materials, Science and Engineering, Parkville, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUCCINYLORNITHINE TRANSAMINASE
A, B, C, D
406Escherichia coli (strain K12)Gene Names: astC (argM, cstC, ydjW)
EC: 2.6.1.81
Find proteins for P77581 (Escherichia coli (strain K12))
Go to UniProtKB:  P77581
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUO
Query on SUO

Download SDF File 
Download CCD File 
A, B, C, D
N~2~-(3-CARBOXYPROPANOYL)-L-ORNITHINE
N~2~-SUCCINYLORNITHINE
C9 H16 N2 O5
VWXQFHJBQHTHMK-LURJTMIESA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C, D
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 183.938α = 90.00
b = 118.264β = 96.82
c = 109.238γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-12-23 
  • Released Date: 2013-01-16 
  • Deposition Author(s): Newman, J., Peat, T.S.

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2013-03-27
    Type: Database references