4UOX

Crystal structure of YgjG in complex with Pyridoxal-5'-phosphate and putrescine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.085 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of Putrescine Aminotransferase from Escherichia Coli Provides Insights Into the Substrate Specificity Among Class III Aminotransferases.

Cha, H.J.Jeong, J.Rojviriya, C.Kim, Y.

(2014) Plos One 9: 13212

  • DOI: 10.1371/journal.pone.0113212
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • YgjG is a putrescine aminotransferase enzyme that transfers amino groups from compounds with terminal primary amines to compounds with an aldehyde group using pyridoxal-5'-phosphate (PLP) as a cofactor. Previous biochemical data show that the enzyme ...

    YgjG is a putrescine aminotransferase enzyme that transfers amino groups from compounds with terminal primary amines to compounds with an aldehyde group using pyridoxal-5'-phosphate (PLP) as a cofactor. Previous biochemical data show that the enzyme prefers primary diamines, such as putrescine, over ornithine as a substrate. To better understand the enzyme's substrate specificity, crystal structures of YgjG from Escherichia coli were determined at 2.3 and 2.1 Å resolutions for the free and putrescine-bound enzymes, respectively. Sequence and structural analyses revealed that YgjG forms a dimer that adopts a class III PLP-dependent aminotransferase fold. A structural comparison between YgjG and other class III aminotransferases revealed that their structures are similar. However, YgjG has an additional N-terminal helical structure that partially contributes to a dimeric interaction with the other subunit via a helix-helix interaction. Interestingly, the YgjG substrate-binding site entrance size and charge distribution are smaller and more hydrophobic than other class III aminotransferases, which suggest that YgjG has a unique substrate binding site that could accommodate primary aliphatic diamine substrates, including putrescine. The YgjG crystal structures provide structural clues to putrescine aminotransferase substrate specificity and binding.


    Organizational Affiliation

    Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTRESCINE AMINOTRANSFERASE
A, B, C, D
467Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: patA (ygjG)
EC: 2.6.1.82
Find proteins for P42588 (Escherichia coli (strain K12))
Go to UniProtKB:  P42588
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, C, D
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PUT
Query on PUT

Download SDF File 
Download CCD File 
A, B, C
1,4-DIAMINOBUTANE
PUTRESCINE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-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: 2.085 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 121.124α = 90.00
b = 129.520β = 90.00
c = 131.273γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-06-11 
  • Released Date: 2014-12-10 
  • Deposition Author(s): Jeong, J.H., Kim, Y.G.

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release