5G4J

Phospholyase A1RDF1 from Arthrobacter in complex with phosphoethanolamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Phospholyase Activity of a Class III Transaminase Homologue.

Cuetos, A.Steffen-Munsberg, F.Mangas Sanchez, J.Frese, A.Bornscheuer, U.T.Hohne, M.Grogan, G.

(2016) Chembiochem 17: 2308-2311

  • DOI: 10.1002/cbic.201600482
  • Primary Citation of Related Structures:  
    5G4J, 5G4I

  • PubMed Abstract: 
  • Pyridoxal-phosphate (PLP)-dependent enzymes catalyse a remarkable diversity of chemical reactions in nature. A1RDF1 from Arthrobacter aurescens TC1 is a fold type I, PLP-dependent enzyme in the class III transaminase (TA) subgroup. Despite sharing 28 ...

    Pyridoxal-phosphate (PLP)-dependent enzymes catalyse a remarkable diversity of chemical reactions in nature. A1RDF1 from Arthrobacter aurescens TC1 is a fold type I, PLP-dependent enzyme in the class III transaminase (TA) subgroup. Despite sharing 28 % sequence identity with its closest structural homologues, including β-alanine:pyruvate and γ-aminobutyrate:α-ketoglutarate TAs, A1RDF1 displayed no TA activity. Activity screening revealed that the enzyme possesses phospholyase (E.C. 4.2.3.2) activity towards O-phosphoethanolamine (PEtN), an activity described previously for vertebrate enzymes such as human AGXT2L1, enzymes for which no structure has yet been reported. In order to shed light on the distinctive features of PLP-dependent phospholyases, structures of A1RDF1 in complex with PLP (internal aldimine) and PLP⋅PEtN (external aldimine) were determined, revealing the basis of substrate binding and the structural factors that distinguish the enzyme from class III homologues that display TA activity.


    Organizational Affiliation

    York Structural Biology Laboratory, University of York, Heslington, York, YO10 5DD, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE AMINOTRANSFERASE CLASS III PROTEINA, B446Paenarthrobacter aurescens TC1Mutation(s): 0 
Gene Names: AAur_pTC20101
EC: 4.2.3.2
Find proteins for A1RDF1 (Paenarthrobacter aurescens (strain TC1))
Explore A1RDF1 
Go to UniProtKB:  A1RDF1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EXT
Query on EXT

Download CCD File 
A, B
{5-hydroxy-6-methyl-4-[(E)-{[2-(phosphonooxy)ethyl]imino}methyl]pyridin-3-yl}methyl dihydrogen phosphate
C10 H16 N2 O9 P2
AKRAFIXJWODRLT-VZUCSPMQSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.166α = 90
b = 96.371β = 90
c = 121.897γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references