4ADB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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, 4ADD, 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINYLORNITHINE TRANSAMINASEABCD406Escherichia coli BL21Mutation(s): 0 
EC: 2.6.1.17 (PDB Primary Data), 2.6.1.81 (PDB Primary Data)
Find proteins for P77581 (Escherichia coli (strain K12))
Explore P77581 
Go to UniProtKB:  P77581
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

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A, B, C, D
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.708α = 90
b = 118.428β = 96.69
c = 109.792γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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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
    Changes: Database references